I don't see how it would affect the cruise, the Liberty only goes to Colon. It doesn't go through the canal at all.
What they plan on doing is adding a 3rd lock that would accomodate the larger ships. It shouldn't affect any traffic going through the older locks.
There will be several shore excursions you can choose from, you just have to decide which way you want to see it, by boat or by train. Either way, the trips are very long. Some of the boat trips only go through 1 lock, but the Panama Canal tour does go through both locks. It starts on the Pacific side and brings you back to the Colon side.
When I went, I took the 2 Oceans By Rail trip. Seeing the canal from the train was great. It took us through jungles and tunnels and we could see the canal constantly with all the container ships going through. I didn't care to see the locks, I live in Michigan and know how locks work.