by all indications, the transporter takes a fair amount of power to operate
Actually it appears that transporters take almost no power to operate. They are among the very last systems to fail (gravity being the last) when power gets scarce; they are available at all flight modes of all Trek spacecraft, from large to small. When the Klingon BoP in ST4:TVH loses power, the two things least affected are the transporter and the cloaking device...
However, it also appears that shields do stop transporters quite categorically. It's not a matter of scrambling the process but of blocking it. And if you manage to bring down the shields of the enemy, why fiddle with transporters? Much better options are now available to you for destroying him, forcing him to do your bidding, and so on.
It might be that transporters still are weaponized - and indeed are the principal weapon of Star Trek. They are called "phasers" and they do the very same thing: using "phasing" technology, they make targets disappear in a flash of light. They just concentrate on the mission-essential, and don't sweat things like reassembly. (But they can do that, too - DS9 and VOY both have examples of the phased beam transporting substances or nanodevices from gun to target!)
Timo Saloniemi