Church Slavonic orthography is quite complicated: there are different letters used to distinshuish between some homonyms, several types of stresses, commonly used abbreviations and all kind of other weird stuff.
Я is a letter from so called "civil script": a variation of Cyrillic alphabet used to write down Russian. It was never intended to be used for Church Slavonic.
Я has replaced two different Church Slavonic letters: ꙗ and ѧ, both of which had their own place in the Church Slavonic orthography and you could not mix them freely.
So if you're asking:
If I replace ꙗ and ѧ with я, will my writing still conform to the Church Slavonic orthography rules?
the answer is no, you can't do that. You have to write ѧ҆зы́къ when you mean "tongue" or
"language" and ꙗ҆зы́къ when you mean "nation".
If you're asking
If I replace ꙗ and ѧ with я, will I still be understood?
then yes, in most cases you probably would, same as if you had written "flour" instead of "flower" in English or vice versa.
However that would be not be standard orthography and some edge cases it could lead to confusion.