I have tried and breaking every pipe in mekanism with a normal pickaxe and a tinker's pickaxe and everything leads to the same crash but it seams to be the result of having mcmp v1.3.0

http://paste.ee/p/iD8Ph

#3952 #3935 and this one is mostly the same issue but with different pipes

This also occurs in [1.10.2][9.2.0.294]

Note: I can whack the pipe a few times without consequence. The crash seems to occur right as the first damage overlay should appear on the pipe.

In the meantime, you can use a configurator in wrench mode to remove pipes and cables.