I don't think it'd be impossible for the Culture to design a FTL engine such that it doesn't use the Warp but is not tactically capable and is such a dead-end developmental path that it's nigh' impossible to develop into a better FTL - they have the databases of thousands of species who've developed FTL on their own using differing principles, after all. Then add some stuff that makes tampering with the engines dangerous, such as making them blow up if someone attempts to reverse-engineer them. That should slow Chaos down enough for Imperium to catch up.