Honestly, that'd just have opened a whole new can of worms. They'd have to actually put them down for good after beating the orks, which would've probably taken the remaining books to accomplish. Nevermind that it was already strange to have that STC thingy in First and Only, and having another source of fresh Men of Iron available - or, in case it'd be from the same source, having that factory survive - would've been just too much of a stretch.
Besides, even just justifying why they were bringing them into the war now, and did not during the Heresy War, would've been tricky. Not even use of the Keys of Hel was sanctioned. Having anybody high-ranking remember about those Men of Iron even existing for realsies in a known location would've been hard to pull off without a lot of plotholes. On the other hand, a lucky find, just in time for this occasion, could've clashed with suspension of disbelief as well.
And then, as said, they'd probably have become an even bigger threat than the Orks, if they had the power to actually defeat them. There was a reason they were outlawed and destroyed.
"The Mechanicus never deletes anything."
It wouldn't surprise me for someone, somewhere to be sitting on forbidden archaeotech.