Option 1 is unlikely, these Sith displayed no skills in Force sight so we cannot make the assumption they have the ability. Granted they may sense a disturbance in the Force, but such a feeling is vague and unspefic, and will only 'work' if biologicals are involved.
The magnetic tracking missiles lock onto a signature that isn't masked by the cloaking device, allowing them to home in on the target regardless of whether the device is activated or not. The only problem is that unless you have a place to fire the weapon initially, it won't know what signature to lock onto. This problem can be worked around in two ways:
1. Sith with particular skill in Force Sight, or sensitivity to such disturbances in the Force, in the CIC can alert the missile batteries when the gravity well pulls the incoming ships back into realspace. They only need a direction and range to lock the missiles on target, and since the radius of the gravity well is a known constant, the Sith only need to provide the direction of the ship they sensed. Death by science.
2. I'm pretty sure that stealth fields can't be engaged when making the jump/transition to or from hyperspace. They're a serious drain on the ship's power plant, and running them continuously during a hyperspace jump (even if it were possible, which is not known for certain) would probably burn out the systems, or put undo strain which could damage them.
So, if pulled unexpectedly from hyperspace by the gravity well there would be a delay while the stealth fields were engaged. This would provide an additional window where the Sith warships could get additional targeting information before the cloaking devices kicked in, further enhancing the missile's lock on their magnetic signatures.
Option 2 is far more likely, your right, hyperdrives take up large amounts of power and as seen in TCW episode stealth fields often have to be deactivated so other systems can operate. Likely G0-T0 would have them cloak moments before exiting hyperspace but as they will be caught off guard in this instance this is not possible.
However were talking about multiple vessels here, several small vessels is likely to minimize potential losses in such situations as these. I highly doubt they'll be able to track the magnetic signature of all of them in such a small space of time and without warning, perhaps a few or maybe only one. Several if not most will escape. Yet this does remove an element of surprise as they can alert the Academy of impending attack.
But concerning the planet itself, when Meetra approached the Academy she did not experience tremors, cave ins etc. granted we have to consider game mechanics etc. and their is substantial evidence to suggest Malachor is unstable. But these seismic events aren't likely going to be occurring all the time, and if they do they are avoidable. Some may be lost but there's plenty more to spare. On the topic of droids, yes they do were down/require maintenance etc. but assassin droids of such elite caliber are likely to be far more sturdy and durable than an average battle droid and likely have in-built repair systems/repair drones - or can be outfitted with some. And let's remember that for G0-T0, money is no object, as I'm sure Warren Stride will tell you. He has a HK Manufacturing Planet pumping out dozens of HK-50s across the galaxy. In this image alone we can see hundreds of units.
I also doubt the droids are going to attempt to stealth their way into the academy, draw some out first, kill them, then charge the place. As you say they'll likely have automated defenses filling that large entrance hall, but then we've got pillars that can be used as cover, and turrets are no match for a Hunter Killer droid. The assassins are likely also going to employ stealth tactics, and then will be caught of guard by anti-stealth tech. This gives the droids a significant advantage as they cannot so easily get up close and are suddenly completely vulnerable to disruptors, particle beam blasters, sonic weapons, concussion rifles, bolt casters etc. the same applies for the Sith who will soon pore into that room and be gunned down. They are completely defenseless against the HKs firepower.
And finally Bao-Dur, I think there are ways he could be persuaded. Firstly the opportunity to destroy the Sith and Malachor V would be an opportunity Bao-Dur would be interested in. But there are other things G0-T0 can offer him too, he could agree to withdraw the Exchange presence on Telos IV, or offer to aid him in driving off Czerka which he could not do alone. Also he could offer to give credits and supplies to the restoration project and the Republic's rebuilding efforts on the whole. However there is also the possibility that Traya could have him assassinated, or perhaps make him into his pawn, and have him sabotage G0-T0's efforts or perhaps even destroy him. Also there is the possibility Traya could escape, both routes need to be considered.
P.S. Concerning the MSG, no there is not any evidence that it is buried in Malachor's surface. But neither is their evidence it is not, nor does the Remote come across or interact with any consoles pertaining to it. We also have to consider that we have no reason to believe Traya has extensive knowledge of the MSG either, certainly not knowledge of its location, or have to move or destroy it. It obviously must be partially underground, else it would be visible from the surface, which it is not. But anyway, to avoid the realm of speculation let's just say to interact with the MSG you need Bao-Dur. Neither G0-T0 nor Traya are well versed in this kind of technology.