This may be the one time I will ever agree with HaKatan on anything, ever. His example is correct, and reading Hebrew incorrectly when Leining / Davening / making a bracha is absolutely a problem. Certainly it can put the fulfillment of a chiyyuv into question (why do you think the Gemara made its statements about the ability to differentiate between Aleph and Ayin?).
Lashon Hakodesh does have phonological rules. Those rules exist regardless of whether the phonology of letters were affected by Galus by way of surrounding existing languages (i.e. vowel shifts in Yiddish), or in one case blatantly ignoring those rules b’shitta because of Maskilim. I have at least 3 sefarim that spell out those rules very clearly.