Regarding designing character classes (if we must restrict ourselves to thinking in terms of "classes" -- sigh) around roles, the bottom line for me with respect to a Star Trek MMORPG is that those roles do not need to be and should not be combat-specific roles. That, IMO, would be dead wrong for a Star Trek Online.
The simplest, easiest approach would be to conceive of ST:O as another combat-focused game, designing Tactical, Engineering, and Science as mere classes optimized for killing stuff, perhaps with specializations to serve in the usual "combat support" functions. Crafting would merely be implemented as a few "tradeskills" that anyone could level up in.
Does this really sound like the right way to go for a MMORPG based on Star Trek? It doesn't to me.
So, if we simply must have classes, I see the more reasonable alternative as letting Tactical/Security and Engineering and Science/Medical be their own roles around which class-appropriate skills can be designed. It simply is not necessary for these roles to align perfectly with tank/nuker/healer -- as long as there are clear roles, so that those kinds of players who like knowing what they're supposed to do can have that information, I think most gamers will have zero difficulty with those roles not being the conventional combat roles.
Let Star Trek Online be its own game. As long as it's internally consistent, deep, and polished, it will have a fair chance to succeed.