Beam arrays are ok... not brilliant but ok... Pushed to their very limits on the games best fed-side tac cruiser (Fleet excel) in the hands of an engineer (Build here) one can just about handle seemingly escort only jobs (Kang duty in CSE, upto 6 probes in KASE, sadly they just don't have the required kick to do all 8)
It can be done even better with a full rack of fleet plasma beams, borg cutting beam and hyper plasma torpedo, the singularity harness set, two plasma damage romulan consoles, max crits with the other consoles and skills, and the kinetic damage proc.
Another advantage of Beam Arrays is the ability to use FAW to clear fighter and mine spam. Anyone who has tried to use CSV to clear fighter or mine spam knows it is painfully difficult, especially compared to the easy mode FAW solution. BO also provides some excellent spike damage which can be either totally devastating with an alpha strike crit (tac captains), or have the only downside mitigated by nadeon inversion (eng captains).
BA are certainly meant to synergize with Engineer abilities. 6-8 beam Nadeon Inversion or EPS broadside can produce quite respectable DPS. Now you can't constantly do this but throw in Red Matter Converter/Weapons Batteries or the new Omega Weapon Amplifier (which are available to all classes) and you can get a high power broadside going a majority of the time.
Now cruisers or other ships with broadside are more susceptible to having their broadside maneuver thwarted due to their slow turn rate. Tractor beams or simply maneuvering on the targets part can take this attack out of the equation. Even then though - they are still able to deliver strikes with half their weapons and without needing to use the tricks above to keep energy levels high, saving them for when they line up the next broadside. This is opposed to Cannon/Turret builds that have a very tight firing arc for good DPS - outside of which all you can do is a little pew pew scratching with the turrets. Target Engine Subsystem, Gravity Well, Viral Matrix, Tractor Beam, Chroniton Torpedo, Borg Tractor Beam, Temporal Inversion Field etc etc etc... There are many ways to make it difficult for those builds to line up on their target even with decent turn rates.
In summary I think the weapons are just fine the way they are. If anything needs to be changed it is DC need to be buffed so there is a reason to use them instead of everyone that knows anything about builds running around with DHC.
You forgot one of the most important advantage beams have: fire at will II & III. With these powers, if you carefully manage your power levels (which is incredibly easy with an eng character) and use batteries, you can almost double your firing rate and increase your dps significantly. All you need is a brain to be able to tank the whole map but it's doable.
Fire at will is a great power in many situations, even in STFs. Probably not everywhere but ifind it way more useful than CRF and CSV, just because your beam will always find a target to hit.
And for the record the best fed cruiser is the galor.