Hello Amber Chancer.
No, the -2 DM is correct and you read it right: That leads to increased damage. Your understandable confusion stems from using the original, 1977 edition of Book 2 as a comparison. In this first edition, pulse lasers were simply cheaper and less effective than beam lasers.
Later on, beginning with the first edition of High Guard in 1979, that paradigm was changed: Now pulse lasers were less accurate, but more powerful. (Based on the idea that they delivered the same energy, but in shorter bursts, I would assume.)
In the revised, 1981 edition of Book 2 it says:
Pulse Lasers fire short bursts of energy at targets and are more effective at
inflicting damage than are beam lasers.
Beam Lasers fire continuous beams of energy at targets and are more effective
in achieving hits than are pulse lasers.
Now, if you like the original idea better, that's cool too. In that case, pulse lasers are a cheaper, less capable option instead of simply a different choice. For roleplaying purposes that might be desirable, giving the PCs an opportunity to upgrade their equipment.
However, I would then simply ignore the damage DM for pulse lasers instead of reverting it to +. Pulse lasers are already disadvantaged because they have lower factors. Even if the DM is just ignored, no warship designer is going to use them (few do as it is, anyway.)
P.S.: You may have noticed that the videogame
Elite used pulse and beam lasers in exactly the same fashion as the original 1977 Book 2 did, with the effect I described above. The player had the opportunity to upgrade from worse weapons to better as they accumulated money.