Assume the security was 'fixed'. Doesn't mean that someone couldn't come and chop the fence with full intention of getting arrested as part of a political protest.
If the known penalty for doing this (even with fully operational security) is light, then that activity isn't really deterred.
The government isn't supposed to deter harmless political protests.
The whole idea of civil disobedience is to get yourself put on trial for something you're willing to do the time for. "They aren't being deterred, the prison sentence has to be increased" is obviously a flawed response to that unless your goal is to suppress dissent without regard to how draconian and disproportionate you have to be in order to do it.
1. trespassing at a nuclear processing facility is not harmless political protest
2. insisting on physical security (i.e. no trespassing) at a nuclear processing facility is not in conflict with the idea of peaceful assembly and political protests
The penalty, must deter future attempts by other people. $1000 and a couple weeks of jail is not going to deter other similar protesters.