I tried KT88's in my CJ 12's. This is the first time I've seen a situation where I did not flat out prefer KT88 over 6550. The KT88 had a bit more power and more full sounding, but the CJ is already by nature full and sweet sounding. I think the 6550 had a bit more detail and nuance at least in my setup. It boils down to what are your other components and your personal taste. If I had very neutral speakers (e.g. Thiel) the KT88 would probably have been a revelation but my Spendors are already warm sounding, and so the 6550 proved to be a better match IMO.
Trying KT88 in the CJ is fun and whether or not you end up keeping them I don't think you'll regret trying it out.
Art
ps: CJ does not suggest using KT88 in the amp. I've spoken with them about it and they just seem to prefer the sound of 6550's with their gear. They don't indicate that KT88 would damage the amp, just that they have not optimized the amp for it.