Since the EGM is tomorrow, I would now just wait to see if the by-law passes. If it does and the committee meets soon after and approves your proposal, all is well. The delay is irritating but not the end of the world.
If the SC does not approve your proposal, there are ways to deal with that if the decision was unreasonable. Even if the new by-law passes and allows the committee to approve applications for minor alterations a decision of a general meeting over-rides any decision of the committee. Similarly, the Tribunal can over-ride unreasonable decisions. So, if the SC does not approve your minor alteration and if their objections were unreasonable, there are ways to deal with it. I suggest you write back here if that happens.
I agree it is more logical that your proposal should have been on the EGM agenda, possibly the last to be approved that way, then the by-law motion. That way, you could have had an approval even if the by-law did not pass. In principle, of course, it is possible that both motions would fail. Or, your approval might have failed but then the by-law passed.
If your proposed alteration is genuinely minor, why do you think the SC is inclined to refuse permission? I cannot think of any reason a SC could have for refusing a kitchen renovation if there is no effect of the appearance from outside or on anything structural. Even if you had appalling taste in colours and finishes and proposed an impractical layout for the kitchen, that would be your problem, not theirs 😉