In a multi-cycle CPU the each of the instructions can take a differing number of instructions.
As you suggested, one of the ways that this can occur is by having an instruction "skip" a pipe-line stage. This is accomplished by having a control unit direct execution of the CPU by having separate execution paths for necessary instructions.
Maybe take a look here for some further information on how a MIPS multi-cycle machine might be implemented.
Generally speaking though, you should take these sorts of explanations with a grain of salt. The sort of machine architecture we learn as non-hardware experts is often quite quaint in comparison to how complicated these things have gotten to the extent that our understandings are often several decades out of date.