I think more information about the source text would clarify the situation.
The Word file at
http://tiny.cc/v88dv is a guide to a Peoplesoft tool for managing submissions to Institutional Review Boards (IRBs) or Institutional Animal Care and Use Committee (IACUCs). "Approved with Deviations from Federal Guidelines (e.g., deviations to consent requirements as described in 45 CFR 46.116-117" is one possible IRB or IACUC decision. This file is the only result from a Google search for "Approved with deviations."
It isn't clear what Micaela is translating, but it appears to be related to approval of pharmaceutical product. If the reviewing body that Micaela is translating for approves applications "with deviations" from 45 CFR 46 (US DHHS regulations), then "deviations" is probably the right choice, but maybe the reviewing body doesn't even consider 45 CFR 46. I think it depends on the context of the text Micaela is working on and who will review it. I spent 2 years with an NGO translating and managing submissions to Harvard IRBs, which did not "approve with deviations". Their decisions were "approval," "disapproval," "deferral," or "modifications required."
I hope this helps.