It's a tough one with the game balance.
I have to admit, I've switched to beam lasers on most of my saved games because I get fed up with the military laser overheating. I prefer the beam lasers punch/heat ratio. It's more statisfying to use IMHO.
I like to make long sustained hits rather than small blasts, and this doesn't really suite the military laser.
To digress for a moment, I made the same choice on FE2/FFE and switched to the 1Mw or 5Mw beam lasers, simply because they were more fun than the big lasers or plasma accelerators. The bigger weapons were simply too powerful.
I'd prefer to have a rapid fire laser that didn't overheat much (sort of a half or quarter power beam laser), but with a much lower effectiveness against enemy shields. Then you could make more of a choice between heat and damage.
Also, I appreciate Oolite isn't 'real' (what, no?

) but todays industrial lasers are in the range of 10 Kilowatts continuous beam now, and their cooling requirements are quite modest. We're only talking 100 times the power (based on FE2/FFE canon) to get to a 1Mw beam laser. In a 1000 years of progress I would imagine that entry level beam lasers would be a very mature technology and cooling wouldn't be an issue. Lasers are actually pretty efficient devices when compared to say engines for example.
I can't really imagine a compelling reason why cooling would be an issue at a relatively low power level of these lasers, when compared to engines which can push you to reasonable fractions of the speed of light or hyperdrives that can flick you across 7 light years of space in a few seconds. Cooling these systems, with their prodigious energy requirements, would seem like a much greater engineering task.
Cheers,
Drew.