Only using known tech might work, even though it is still going to be pretty suspicious if they really are using tons of facsimile archaeotech or even just abnormally high quality tech, especially if they're supposed to have been kicking around for a few millenia. The Imperium has seen enough Trojan Horses to know when to look one in the mouth, if you can follow that butchered aphorism.

The thing with the Geneseed though... I get the Culture has picotechnology and instant flawless cloning and everything, but they really shouldn't be able to replicate Geneseed. That's just so wrong, it's hard to even explain. I'm not saying they couldn't do it, but that's just so un-40K it's depressing.

My suggestion, other than applying the Culture's weaknesses to Chaos, is that the IoM desperately needs a power boost. Giving them an STC via Emperor ex Machina and/or just waking the SoB up is really the only option to keep it even remotely competitive. Otherwise this is just a slo-mo demolition of one of the most interesting SF civilizations by one of the least, and that's really really sad.