Yeah you're probably going to want to remove those little popcorn bud sites; they're harder to harvest and take away potential energy from the larger, higher main colas. When you cut these what basically happens is that the main colas get huge because now the plant is using all of its energy on them. Whereas before it was split between the main colas and the smaller bud sites. The key though is to do this gradually because as you guessed this can definitely stress a plant. What I would do is trim away in levels and just work your way up. Also take note of where the light is actually penetrating the canopy/leaves. If they're not getting much light, they're not going to be worth it come harvest time.
IF you're going to remove any, I'd say do it sooner rather than later. When the plant is in its later weeks of flowering you're going to want it fully devoted to bud development, instead of dealing with bud sites getting removed from it.
She looks beautiful by the way!