Well, it's already been said that gauss-armed ships are useless for spacefight except for siege battles (incl. besieging "asteroid" capital ships of the UWM). So - no, probably not...
What about making a test run of FEL-ships? Without any fancy materials they might be less crucial to lose (as in, if UWM somehow gets its hands on them), but by sole virtue of advanced design they offer an edge compared to UWM ships of comparable size.
(Somehow, for some reason, I feel that the time UWM throws its best attempt at capturing new ship technology, it would not be in pitched battle, but in an ambush - or, better, with a well-planned sabotage/capture intelligence mission. It might (or might not) wait a little until we've actually fought their fleets head-on, which depends on their carelessness and spy network among Allied worlds. But - we might want to tighten the security on the ships we intend to station "out of immediate reach" just for that. We might be unable to stop a good black-ops mission, but we probably can screw it up enough and maybe buy enough time to enact self-destruct or something - going for stalemate.)
On the other hand, even if we put no advanced new armor on FEL-cruisers (hoh, Felcruisers!), the overall chamber system might benefit from the new materials, for example (as Paris earlier pointed out, maybe pure-Hex can even reflect X-rays or something, allowing for new and interesting ways of upgrading the design).