I don't think so - I think it was also intended to punish the population. Containing a potential threat from Hamas would not require the kinds of measures they undertook such as imposing fishing restrictions on them which severely hampered their economy and effected, most directly, the average Gazan (just one example). Hamas won in a legally recognized election that was fair by all accounts. Hamas has always been there - it didn't suddenly pop up with elections.
I truly believe that for every specific restriction on Gaza, like your example with the Fishing, has a reason.
Just because we don't see articles about Hamas or regular Gazans using the water to promote their terrorism, doesn't mean it's not happening. These restrictions cost ISrael time, resources and money, so you can bet there is a reason for them .