They wouldn't be just cannon fodder, plus we send sentient creatures to death every mission without batting an eyelid, so don't go bringing morality we don't have into this.
I'm not. I think normal-level cogs (not the 1 sidekick, but ... I'll call them splicogs for now.) made from the design of this 'prototype' would be greatly weaker than any of our existing cog designs, and the benefits they might 'also have' are extremely limited. We can already send the goo girls into somewhere if we want stealth (Chemista was introduced originally with a description of how to use her that included breaking into banks secretly).
We already lose cogs faster than we can make them, with our normal playstyle. If we make cogs that 'go hide' instead of 'tank damage', we are not strengthening our forces at all. Those cogs won't be coming back if everyone else over them dies. Part of the reason for those cogs is so they can die first.
What other powers does this splinter cog have, if kept as a sidekick? We don't even know yet. We could take him initially and temporarily as a sidekick - then later decide, ehh, he's better off as scrap, whether we want the design for splicogs or not. We can always do that.
Don't forget, this cog's been stealing at least several of Cerulean's staff-in-progresses for some time now. Has he been stealing other things too? Don't we at least want to know what treasures he's hoarded?
Don't destructively ask for a bunch of pale and far weaker, less useful imitations before we know what the original's worth. Right now we don't even know what we're asking to destroy.