Is there a way to capture via irScrutinizer and the pronto remote?
Unfortunately not directly. Once I planned on implementing it, but scrapped the idea after all, see
[Link: github.com] if you are interested. Indirectly, you learn in the Pronto, save it as CCF or XCF, and import that file in IrScrutinizer.
Disabling repeat finder is meaningless in this context, since the Pronto has its own "repeat finder", which, to my knowledge, cannot be turned off.