There were several reasons to steal the bankais, even if they're more powerful without them. First off, it's demoralizing to the Captains. Possessing a bankai is one of the things that set them apart from the common soldiers. Secondly, while it may have weakened the Quincy, it severely weakened the Captains, since sealing their bankai took away a large chunk of their power. Third, it served as a distraction to the Captains, instead of focusing purely on locating the Quincies and bringing the fight to them, they had to find ways to recoup their power.

So, I'd say it worked out well for the Quincies, despite the temporary cost.