I'm sure shields are by nature very dynamic things: they simply cannot be built to be static, but instead have to consist of complex overlapping cyclic things with various characteristics, some good, some bad.
What O'Brien achieved would probably not help an enemy destroy the Phoenix in a real tactical situation. For all we know, the technique requires the target ship to remain perfectly still, and to refrain from rotating or otherwise adjusting the shields during the process - and the beamover might take something like fifteen minutes. (There's an intriguing passage describing a similar trick by Klingons in the novel The Final Reflection.)
As for using transporters as weapons... For all we know, phasers are transporters, only rigged a bit differently. According to ENT, human phasers emerge roughly at the same time humans master transporter technology. They also behave much the same vis-á-vis shields. And we hear in VOY and DS9 that phaser beams and their alien counterparts can be used for transporting physical things like poisons or nanomachines.
I don't see much advantage in using a conventional transporter for delivering the destruction, when it in practice works the same way as a phaser beam: it's line-of-sight, cannot go around corners, cannot penetrate shields - and apparently requires more complex subspace trickery than phaser beams do for becoming faster-than-light.
Timo Saloniemi