Discussed here many, many times. A full transit is always more desirable. You are missing, unless you take an excursion that completes the Canal on a ferry, about 3/4s of the distance of the Canal.
There can be logistical issues for some people in terms of one way flights to start of cruise, or home from ending. But, IMHO, not really that big an issue.
But if all you can do is a partial, go for it.