^ Typically, I think a tractor beam might be most useful in preventing a smaller ship like that from pulling off such a maneuver, but the writers went out of their way to specify that the defenses of the Dominion ships kept a tractor beam lock from being achieved.
As for using pulsed fire from the regular phaser arrays, the TNG TM suggests this is possible but that achieving maximum beam dwell time is more often the most effective solution. It also suggests that phasers can fire for 45 minutes at a time or something, so with that on top of the vast numbers of emitter segments, I don't think there's any Gatling envy going on.
I don't think specific close-in weapons systems are likely to be a big deal for starships; microtorpedoes are really tiny and it's hard to imagine they are viable for ship to ship combat between full-scale starships, especially if they use chemical warheads and such as suggested in DS9 TM. Moreover, "dirty" weapons like torpedoes that appear to detonate omnidirectionally are too dangerous to use close in to the ship that launched them. If a ship's phasers detonated an incoming torpedo at close range, they'd still end up absorbing most of the energy from the torpedo's explosion; according to the whole "photon shock wave" thing or whatever that was when they fired the phasers to detonate the torpedo instead of just having it detonate normally, it might even be worse. I guess this explains why we don't see them doing this. Shooting down torpedoes at extreme long ranges may be viable, but the torpedoes do, after all, move very fast...even if VFX seems to enjoy giving us the slow-motion version for added drama
Suicide runs like that are extremely unusual and our heroes were shocked by the maneuver and how unnecessary it was, as we were to be. Aside from the expected tractor beam, I wouldn't be surprised that they didn't have a whole lot in the playbook about this, or at least lacked time to implement something else. Then again, many of the powers may use something akin to the Mars Defense Perimeter flying bombs setup to defend some locations, so it may be an issue.
It does at least seem clear that over the following few years, they found ways to at least partially deal with a lot of the Jem'Hadar tricks (e.g., the shooting/beaming right through Federation shields, the tractor-proof shield configuration...).