While I think religious freedom is imperative and people should be allowed to practice their religion without persecution, if this leads to pie banning, shame on religion. But, on a serious note, when religion creeps into the broader population forcing the wishes of some onto the lives of many, I find that to be seriously problematic.
If religion makes a person ban the eating of pie, religion leads people to do some strange things. People think that they can control other people, all in the name of religion. People should be able to decide for themselves how to live, as long as it doesn't hurt other people.
Yes, religion plays too large a role in society. Religion has a place in the houses of worship and homes of the individuals who follow these religions. However, not everyone is the same religion. This means that when one religion dominates the discourse, many people who do not follow this religion become disenfranchised.
No, religion does not play too large a role in society. The story of Oliver Cromwell, cited in the question occurred in another time and place when there was not separation of church and state. Today, in the United States especially, we have laws in place to maintain a separation between church and state. It's a delicate balance and churches often try to insert themselves into government, so we have to be constantly vigilant to protect and maintain the delicate balance.