The procedures for amending the constitution are within the document. I doubt they would have given ways to alter the document without believing this was a possibility. Also, the first ten amendments were drafted the same year the constitution was implemented. It's hard to claim they didn't foresee amendments being part of the process. However, they probably didn't expect it to be common place as they created tough standards to get amendments passed. Nonetheless, amending the constitution isn't really done commonly and I would argue it isn't really going against their intentions.
As for religion, it is true that the founding fathers believed in a deity, but there religion beliefs were diverse and many were secular. Thomas Jefferson and Ben Franklin were both prominent deists who believed in secular government. The separation of church and state comes from Jefferson and that's why republicans fought to remove his name from textbooks in Texas. John Adams was a strong Christian, but he was a Unitarian who believed that religion was a personal thing and should not be promoted by the state. This is reinforced by the Treaty of Tripoli which was drafted during his administration. George Washington is ambiguous but I would say he was likely a deist because of his strong ties to masonry. However, there are claims of him praying and attending church. The only major founding father that would have rejected the separation of Church and state is Samuel Adams. So, we can look at the founding father's religious beliefs in a historical sense and appreciate it. Yet, it does not effect how we view the separation of church and state because the intentions of many of them were clear. It's like France and Italy. They have a fairly religious background, but there current government and state policies have been fairly secular. Religion is fine when it remains in the private sphere. When others try to dictate policies because of their personal religious beliefs, I have to cringe. That is why the transgender community doesn't get treated equally and that is why we don't get equal rights. It frustrates me.