I guess the only way to mate Mikrotik and Fibers right now is using x86 equipment and intel network cards with SFP slots on them.
There is no such thing as a mini-pci SFP, to be honest the PCI bus would be way too slow for Gigabit Ethernet anyways.
Sooo.... just put up with one of those so-called "carrier-grade" fiber converters, otherwise be prepared to fit a 400$ network card into an x86-based machine
PS: Even the SFP itself can be seen as single point of failure... and SFPs (from my experience) fail way more often than really good fiber converters.
Still, the SFP is a more elegant solution to the problem