SharePoint isn't the only Microsoft technology that breaks when the "FIPS bit" is enabled. With that said...
In my experiences, government customers have applied the FIPS 140-2 requirement to encryption of data at rest and in flight. As long as they've selected a FIPS 140-2 compliant/validated at rest encryption solution and properly configured SSL for their sites then they seem to be okay (see 2nd paragraph). CipherPoint offers one of the handful of available solutions that will encrypt SharePoint content at rest using FIPS 140-2 validated cryptography.
Many of our customers have had to get their SharePoint farms through the accreditation process and while I haven't been personally involved in that effort from start to finish I do know that the DISA STIG comes into play. I don't think the STIGs are instructional - I like the NIST SCAP for SharePoint as it's a very easy to understand hardening guide.
To my knowledge there is neither a STIG nor a SCAP checklist for SP2013.
Finally, the link below would appear to be Microsoft's stance on this matter:
I know some folks that have been through the accreditation process. Let me see if I can get one of them to post.