Is this a one-time problem?
If you have mariculture, which im sure you dont, that mod has a ladle that can remove tiny bits of liquid from containers. (and store it in the ladle to move elsewhere)
If you have gregtech, that mod has a plunger that can "delete" leftover liquids in containers (but not move it elsewhere)
If its a one-time problem, you can just break and replace the container. In this case I imagine breaking the controller itself would do, or pipe the contains into a tank of some sort and break/replace that.