Concerning attacking the Trayus Academy, firstly the battle by no means has to occur inside the Academy. The best tactic will to be set up a 'blockade' in the large open space before the entrance. And then cause some ruckus to draw them out. This gives them an advantage as any Sith venturing out of the Academy will have to do so through a single small entrance, and will walk straight into awaiting blaster fire. This also gives the attackers the advantage of range, putting the Sith at a disadvantage. It will also give the inhabitants the false illusion they are attempting to lay siege to the Academy and preventing anyone from reinforcing the MSG. And lets remember if G0-T0 gets hold of some anti-stealth tech then the stealth generators will become useless, so they cannot sneak behind enemy lines.
So instantly the Sith lose the advantage of close-quarters combat, in order to bring their weapons to bear they have to get up close. Sure they have Sith Commandos with blasters and grenades. But they'll be going up against mercenaries, assassins and droids with the best tech G0-T0 can outfit them with. We're talking:
- Stealth generators so they can get in close and avoid detection en route to the academy.
- Disruptor rifles that pack enough punch to disintegrate their enemy with one shot.
- Rocket and grenade launchers that will deal heavy and indiscriminate damage to Sith and troopers alike.
- Particle beam blasters which launch particle projectiles which explode on contact, making them impossible to deflect via lightsabers.
- Sonic weapons which generate highly-focused bursts of sonic energy which pass through lightsabers and rupture internal organs, and lower settings (sonic screamers) could cause disorientation and loss of consciousness.
- Concussion rifles often favoured by Trandoshans that fire compressed capsules of ionized air that send powerful shock waves on contact, sending opponents flying through the air and bypassing lightsabers.
- Bolt casters which spew electrical energy at the opponent and can hit multiple opponents, and once again bypass lightsabers.
- Flamethrowers and carbonite projectors, if the enemy tries to get in close and hasn't yet been gunned down these will finish them off.
Now as you mentioned a lot of these weapons are indiscriminate, but given that the attackers will not be fighting in the academy but outside it with their enemies infront and allies behind, it won't be a problem. All the indisciminate chaos will be targeted at them. What's more the HK units, equipped with stealth generators, can plant some mines in front of the academy before they engage, effectively turning it into a death trap.
But if the Sith forces to manage to get in close (which is highly unlikely), the attackers are still capable. I did not make up the term 'piercing touch', its part of Gand martial arts:
The Gand findsmen utilized a style of martial arts, of which the tenets were not readily understood by the galactic community. A few of the moves were translated and described, however; Piercing Touch and Striking Mist. The former, Piercing Touch, was described as a powerful punch that was able to penetrate bone, chitin, and various armors. This move was demonstrated by Ooryl Qrygg when he punched a hole through stormtrooper armor while stationed on Talasea. The other move, Striking Mist, allowed the attacking Gand to sneak in close to their opponent, so that the hits could not be parried or dodged. ~ Wookieepedia, Gand martial arts AKA close quarters fighting.
Now I'm no expert, but if a Gand manages to get up close to an assassin, and uses piercing touch, there is nothing that assassin can do to stop him. At close range he cannot bring the tip of his pike to bear, if he raises his pike in defense the Gand will punch through it (hence it will break) and slam into his chest. Dead assassin.
As for Trandoshans, let's remember that the stun module is at the tip of the pike, so a Trandoshan with wall stature and long arms can dodge the initial jab and then respond with a thwack to the unelectrified part of the pike, or simply grab it and wrench it away. Both leave the assassin open to attack.
What does pose a problem though however, is the MSG, has you said it could have been rendered inoperable. However the MSG is likely buried into the planet's crust as it managed to survive the destruction of the planet despite being at the center of the chaos, so destroying it completely will be very difficult. However the caves could be collapsed, and yet it may not be in Traya's best intentions to do this as the MSG provides her with a means of destroying G0-T0.
Another problem is getting to Malachor V in the first place. However the point you make about stealth generators would only be valid if this battle was occurring in a different era where supply of stygium crystals were rare, and other less crystals such as hibridium would be used as substitutes. However in this era stygium has not yet become rare and therefore is likely to be used as stealth tech. Negating the disadvantages of 'double-blind'. Lets also remember that not all Sith had the ability of 'Force sight' and likely only Traya would be able to see through cloaking devices. Evident through the fact that Meetra could not see the cloaked assassins, the Jedi could not see the Emperor's cloaked space fortress, neither could they see Maul cloaked Scimitar despite it flying right over the Jedi Temple and Anakin almost walked into a stealth ship during the Battle of Christophsis.
And luckily G0-T0 has lots of droid pilots able to navigate Malachor's storms, either that or jettison transport pods disguised as falling debris. However you make a good point about interdiction, that is after all how Traya defeated Exar Kun in the last battle and could definitely be applied here. But lets say G0-T0's little stealthed fleet is pulled out of hyperspace en route to Malachor V. For one they will remain stealthed so Traya will have no means of knowing whether they have been pulled or not, and from that point they can simply skirt around the ships in realspace until they exit the interdiction field and then jump to hyperspace again. Simples. *eek*