HeathenStorm brings up an interesting point. You also have to consider that Cryptic is having enough problems with server restarts to keep everything stable already. Imagine how big the load would be if this game were opened up to the masses on Steam? Yeah, I'd rather they stabilize what's there now before they put it up on Steam again.
There is a way to get it to launch through Steam, however.
Find the game directory. In the folder that has directx_aug2009_redist, localdata, reslists, and CrypticError.exe, you'll find a Star Trek Online.exe. This is the game's launcher. If you add it to Steam, you'll be able to play the game through it.
When the game releases on Steam, simply take that game directory folder, cut and paste it to steamapps\common, then go to the game's Store page and tell it to install it. It will detect that the files are already there and finish within a few minutes.
I wouldn't expect to see the Steam version come back until Summer at the soonest. I have a feeling they'll hook up the accolade system into the Steam Achievements system and maybe even offer free items if you join though steam. I know champs ran a promo with steam that if you signed up they gave you certain goodies.
Also if STO came out during the Steam Summer sale it could be part of the contest they usually run. I could see a simple goal in STO earning you Coal/tickets for what ever event Steam is running. This would cause tons of F2P folks to show up even if its just for that one reason.
I have a feeling Cryptic still has seen its bump in members due to F2P launch, and will see a 2nd bump due to the FE and 2nd anniversary. Daily patches and restarts is proof enough they are struggling to keep up with the new accounts. I'm sure they'll wait a few months to get stuff stabilized then offer the game on steam for that 3rd bump in membership.