I'm going to assume you're talking about "specific Tiles" that you're adding. You may be interested in implementing IFluidHandler rather than IFluidTank, because the handler is what pipes connect to, and the handler methods include ForgeDirection arguments, so you know which side of the block is being drained from, so you can check the TileEntity on that side.
If I understand the bit with BC wooden pipes correctly, you're worried that one could use a plasma-compatible pipe as an intermediate, which you don't want. To solve this, just add the same logic you'd have in the machine to your plasma-compatible pipes.
Hope this helps.
Yeah sorry, I should of been a little more specific. I didn't know the drain method in IFluidHandler has a direction parameter, so thanks a lot for pointing that out. That will most likely solve the problem.
The only thing I'll have to look into though is how this effect the machines in GT, but I'll mark this as solved for the moment until I get around to testing it.