Banshee, as to your questions, I haven't messed around with TS or BCCS in a little while (busy and all that) but your description of baleful polymorph as blending shapeshifting and destroy seems creative to me and I don't see why you couldn't make it work.
Alternately, you could forgo doing damage with Destroy and have the Destroy aspect alter stats to those of whatever you are polymorphing the target to since Shapeshift allows you to retain your own ability scores regardless of form. Essentially using Destroy to break down the target's own physical consistancy so that it becomes, entirely, that of the desired creature.
I personally would be tempted to add an extra DC cost to make it permanent and/or non-dispellable - Or have a certain damage threshold you needed to hit with Destroy in order to make it permanent, otherwise it is a timelimit in rounds/hours/days/whatever - there is a lot you could do with it. This falls into the realm of creative tinkering, definitely.
A lot would entirely depend upon what kind of DC you're looking at to begin with. Blending tends to skyrocket DC's, so it may be sufficiently high just by virtue of that alone.
