Orthography influences pronunciation. In time people will start pronouncing those words as the orthography suggests rather than deducing it from the context.
is there any evidence for that?
anecdotal evidence in english for example suggests just the opposite: light -> lite, etc
however learning a language as a child growing up, vs as a second language later are quite different, and the dynamics that affect language change are hence very different too.
http://jbr.me.uk/ranto/m.html explains how esperanto is unlikely to change, and also why that would be a good thing.
back to your argument, i don't think the words with different pronunciation would be lost, but certainly the language would be harder to learn.