I went all light side on my IA, and with the exception of people in flash points getting pissed when I won rolls that caused a light side branch there were no issues.
Pretty much this. I'm Light V, having picked most of the light options as I went up (but NOT all of them, since some of the Light options are just stupid), and with Diplomacy being my mission skill I can shift alignments easily. Here's what it's done for me:
> I use a blue color crystal in the gun that I hardly ever use instead of the red/orange ones.
> I use a +defense or +alacrity activation effect for my Relic, instead of the +crit ones. (I went with +defense.) In PvP the offensive ones are probably more popular, but as someone who soloes PvE a lot, that defense boost can be huge.
> I could have a little sandcrawler pet that has no effect, instead of the hovering interrogation probe that has no effect.
> There are a few custom armor pieces that I could buy, even though there's no actual reason to do so and by the time you'd be able to afford them you'd be nearly to the point where you start worrying about set bonuses.
The only downside is that in most Flashpoints I end up taking choices that are relatively unpopular with my teammates. In PUGs this doesn't really matter, but if you're doing cooperative story missions with friends it might cause issues.
But also realize that each of our companions have their own biases, and very few of them really LIKE evil choices. One companion likes anarchist choices (which can sometimes be light, depending on the situation), one likes "clever" choices, one likes "patriotic" choices, and one just outright likes you being nice to people. So you might actually get more companion influence boosts if you take the light paths, depending on which companion you're using (and assuming you're using companions for PvE).