Except in the war they were a hindrance, the time that could have been spent fighting the reapers is wasted by fighting Cerberus. If they were morally grey they would still do questionable things but they wouldn't be hindering the fight against the reapers.
Well then, pfft, maybe we should have stayed with Cerberus and controlled the Reapers!
*goes to Mars*
*helps EVA kill everyone*
*builds Cerberus Crucible with an indoctrinated slave army*
*MUAHAHAHAAHAHAHAHAHAAHAHA*
But we still use Cerberus assets. Continually, their actions and constructions do help Shepard, even to an essential extent. This maintains through all 3 games, it just is little-known in ME1, and is more challenged in ME3 instead of reinforced as a concept (in ME2 it was a focus of things).
EDIT: They ARE morally grey as an organization (even if maybe cartoonishly bad as people by the end). Their actions (something many forms of morality focuses on, as opposed to intent) do ensure Shepard's success. Their pursuit of human advancement made sure, by intent even, that we were able to challenge the Reapers. You can condemn so much of Cerberus, but as an organization, they were written to be essential to Shepard even getting to complete the Crucible. And not just for 'existing and doing their thing', but for actively trying to help Shepard fight the Reapers and Collectors. ME3 shifted away from this aspect more, but their Greyness did continue in a way, through how they ended up technically right (at least if we believe certain things) about the Reapers and their mechanisms and how we could harness their power instead of waste it.
But yes, their Greyness eroded more by the end of ME2, and by the end of ME3, it was nearly indisputable that they were Bad. This is a trend in the writing that I've seen many hate.