The more I think about it, the more difficult it seems to simply "fix" repair kit without changing it mechanically. The only way to make an orb give more armor without changing the pickup rate is to make the full pickup time take longer. This seems simple enough by itself, but the problem is that every mech on the field draws from the same pool of HP in that orb. If an orb had 170 hp in theory a mech with advanced repair kit should be able to draw 212.5 armor from it, but what happens if that ARK mech pulls 171 armor from the orb then leaves? Another mech ARK would, I would think, be able draw off that remaining 41.5 armor, but not a mech without. And what of a mech with a regular repair kit that can draw a maximum of 191.25 armor from an orb? What happens when a mech with ARK is standing the same orb as a mech without?
It ends up being a whole mess of how you communicate to players if and how much they can pull from orbs, and how you handle the remaining balance of armor heals. One thing you could do is have orbs leave a 'ghost orb' on depletion that can only be picked up with a repair kit, but that seems a little contrived.
Something you could do with repair kit that would disassociate it from orbs without requiring a name change would be to make it do something with the repair drone, such as faster drone deployment when overheated, below 10% hp, near teammates, etc. This one makes me nervous however because I distinctly recall faster drone deployment being a staple when it was available in the skill tree, so I hesitate to advocate for it without a distinct recollection of why that was removed.
Another alternative that should do a lot for the PTFO people would be to give a small amount hp/second when near a teammate that is repairing, on an objective (perhaps only one you own, only one the other team owns, whatever), and/or while pulling EU from a tree. I think the heal amount would have to be pretty small (on the order of a few hp/second) for this one to be balanced, especially heals while on an objective.
Honestly though I'm not a huge fan of any of the repair kit fixes above, and I would prefer some of the reworks for extractor in their place. Perhaps someone else has a more clever solution.
Going back to extractor, and in keeping with the original idea of pulling armor off of orbs even when at full, perhaps you could make extractor consume orbs to reduce heat when at full armor. Wouldn't even have to change the name.