The thing what the GTVA had to state is: "We cannot be sure whether beams are capable of surpassing the Lucifer's shields."
In this case, the Colly might have been unable to act in its main role, what, if you ask me, is way too great risk at a ship built for 20 years.
Since we're all providing suppositions of various sorts, I've always operated under the supposition that GTVA Command is at least intelligent enough to not invest twenty years and myriad resources into a massive project like the Colossus without being just about certain that it would be capable of defeating its primary target.
The GTVA had detailed scans of the Lucifer's internal systems from "Playing Judas" (and other similar efforts, most likely), so they had to have a good idea of its mechanics and overall power output. Also note that the FS2 tech room states that the Lucifer's shields were "impenetrable to all weapons at the time," which would seem to indicate that this is thought to no longer be the case. Whether or not the Colossus's main beam cannons would penetrate the Lucifer's shields without being affected at all may be up for debate, but I feel fairly certain that they would have done a significant level of damage even in the worst case.
As for the Lucifer's armaments in FS2, I've always assumed that those SReds were just a matter of someone at
sticking some beam cannons on the model, since the ship never appeared in the retail campaign anyway. To have any sort of accurate match-up between the Lucifer and Colossus, I think you have to go back to the Shivan Super Lasers, or the equivalent SSLBeams that the FSPort developed.
And as for fighter-equipped beams...if you could tell the GTVA how a fighter-size reactor would be able to power a beam stronger than a weak AAA, or how such a beam and its heatsinks could be made small and light enough to practically mount on a fighter, I'm sure they'd love to hear it.