Yes, troops now improve planet happiness. Which is kinda odd to see in action, because the largest concentrations of troops are on worlds you'vejust invaded. So now, instead of a world being "angry" or even "rioting" after you've just taken it, they are often "happy" or even "jubilant"...weird.
I think there needs to be some adjustment for relative races or something. If troops could only bring alien race happiness up to "neutral" level but not further you'd have a much more realistic effect.
And, yes, I've been asking for a "pacification" intel op for ages. Like everything else related to new features, it's catch-as-catch-can while the AI and assorted bugs are being worked on. Who knows when and if it will be done.