Letter of Recommendation from an unofficial college email ID
“Will it harm my application?” — Maybe, maybe not… it depends on the mindset of the persons who will review the application. The likelihood that it impacts negatively your application is probably not very high (there are more people than you think, even in non-rural non-Indian areas, who use commercial email accounts rather than institutional ones).

However, you are right there is some slight risk: there have been recent cases of people using faking email accounts for other researchers, e.g. in order to increase their chances in peer review. Because these cases have been publicized recently, people may be more wary of non-institutional addresses.

But more to the point: what can you do? — Not much. If the format  of the letter is free, ask your letter writers to use official letterhead from their institution… Otherwise, try and see if your letter writers are listed on their institution's public pages, at least, with their email address: that way, the person receiving the application will be able (if he wants to) to check their identity.