I'm drawing a blank here, if the loan amount increases as a borrower-request, the origination fee may increase as well due to change of circumstance, or is it still a zero tolerance item?

If it's a valid change in circumstance, you can reset your tolerance basis for related fees.

You can't just raise the origination fee because you raise the loan amount tho, unless your fee is directly tied to the loan amount, ie, points.

Truffle, in this instance the borrower decided to decrease their down payment and wanted the higher loan amount. The origination fee is 1% of the loan amount. So in this case, with the change of the loan amount the origination fee goes up as well. Would we be permitted to charge this amount to the borrower or are we stuck at the original origination fee amount?

No, it is a borrower requested change that has caused the increase in the origination fee as it is based on the loan amount and would be considered a valid changed circumstance.