MEChimpanzee and
raju1212:
This issue is not a big deal so long as you have two references from people who you trust and who will vouch for you with the utmost confidence. That is the most important consideration.
Since MiF programs tend to take folks with little to no professional experience (coming out of undergrad), an academic reference or two often makes sense. There are candidates who do have full-time professional experience and are therefore more removed from their undergraduate studies. In those cases, supervisors or work colleagues might be more appropriate.
The admissions committee recognizes the range of candidates. A candidate submitting two academic references is not in an advantageous position compared to another submitting two professional references or a hybrid.
As long as it's not a requirement (and instead a suggestion), you can really pick whomever you want and you think would be best given your relationships, experience, and overall profile strategy for your application.