The trade-off has variable value depending in exactly where your base To Hit number falls on the 2d6 Gaussian probability bell curve; if, all DMs accounted for on both sides, you are looking at 6+/7+ or less To Hit for beam/pulse respectively, the less-accurate, more-damaging, cheaper pulse laser (a/k/a/ blaster) has the edge in dealing damage efficiently, but if you are up against a really tough foe and your base To Hit after all DMs is up around 11+/12+, you are going to wish you had beams (a/k/a/ heat rays).
I stick with the as-written -1 for pulses in Anti-Missile fire; making them half as effective against incoming missiles for half the price is good enough for MTU -- I don't want to be perceived as actively discouraging their use by PC types. Especially since the second damage point (or roll, if you interpret it that way) is essentially wasted when shooting at a missile.
And of course, the pulse laser is standard equipment on a Type J precisely because doing more damage, it is more efficient at cutting into large, stationary objects at point-blank range; a selling point for some...