I was just thinking about this when I saw the thread.. While I'm sure the OP was well-intentioned. here's my idea.
Why not add to the Immersion to the IP, and give Cruisers a slight increase in Beam Damage, but at the same time slightly reduce Torpedo Damage to compensate?
A-La the "Sacrifice of Angels" scene where Sisko orders the Galaxy sqadrons to point blank. and we see the massive Beam arrays lighting things up like the 4th of July.
Also, i would say for balance's sake, give escorts a slight bump to cannon dmg, and torp dmg but reduced Beam damage as a result. Giving them a more "Defiant-esque" approach.
For Science Ships (not sure how this works for KDF, but..) they could bet given a small boost to healing / science specific abilities.. like a +2 to main deflectors, or emitters.. etc. and a reduced torpedo yield to compensate and avoid being overpowered.
While I like the WoW-in-Space tank, DPS, Heal model they're aiming at, it fits, but not in the nice-neat MMO way they were envisioning at the start.