What does "If that's the culture on the bottom, God help the culture at the top" mean?

To say "God help" people or things does not necessarily imply that the speaker actually believes in God or is religious. It is a commonly used phrase meaning that the person(s) or thing(s) are in big trouble or have a problem so big that only "God" can help them (i.e. human power cannot). Examples:

That building is burning and people are locked inside, God help them!

God help you if I catch you stealing from me!

In the example you quoted a janitor said that he was afraid to report the sexual abuse of boys because he believed his supervisors would refuse to listen and force him to leave his job. A janitor is a low level employee who cleans toilets etc. Freeh is saying that if the lowest level employees were afraid to speak out because they knew their bosses would put the reputation of the university before the welfare of the young boys, then the problem (the culture of secrecy) must surely exist all the way to the top of the organisation, where it would have been impossible to overcome.

Thank you, Contrex.
Does "God help the culture at the top" mean "May God help the culture of secrecy at the leadership of Pen. State" then?

Yes.

It means this, O,

'If the people on the lowest levels are so afraid to confront the people on the highest levels about something as important as the sexual abuse of children, then there is little hope that the people on the highest levels will ever know just how lacking in moral authority they are and, if there is a god, they will face that god's justice and anger because of the way they made the people afraid.'

"If the people on the bottom live in fear, the people on the top are standing on a false foundation and will fall."

Those are my two best tries at explaining the phrase.

Joe(cheers)Nation

Excellent!
Thank you Joe.

Sorry Contrex. I've reselected Joe's reply as the Answer.