I strongly suggest that you not read between the lines. Accept what ever someone says at face value. If you think there is some hidden meaning ask about it.
Weddings are primarily adult functions. I agree that leaving your very young (4 1/2 and 20 mos) children at home is the best thing to do. They will not enjoy the wedding and in fact may not do well having their routine upset. The in laws, who would perhaps ordinarily enjoy seeing them, will be involved in the wedding and not have time for them. Besides, it sounds like they will be visiting you soon and will be able to enjoy them then.
I strongly believe that we need to make decisions based first on our own needs. We should consider others wishes but should only act on them if doing so does not take away from what we need. You do not need to sacrifice your energy, money, time to meet the wishes of the rest of the family.
I'm actually not clear, here, what is actually needed and what is just a wish. Your daughter as a flower girl is not needed nor does it appear that it a strong wish. "if, she wants to be." I think you've come to a reasonable conclusion based on what you wrote. I'm not sure about your mil's offer to pay for her air fare. You've said nothing to indicate to me why she made that offer. Except for your comment towards the end that your inlaws will consider you to be inconsiderate. I think that if they think you're inconsiderate that they are inconsiderate. You are adults responsible for your children. The decision is yours to make.
Your post does make it seem that it's important to have equal family representation as if the two families are in competition with each other. Do you really want to get into that game? It's like "keeping up with the Jones." No one wins and everyone eventually loses. Love and concern for each other is what works to keep families together.
You are being reasonable. Perhaps it will help if you and your husband are clear and united about your decision you will feel less anxious about your in-law's opinion. I suggest that if you give specific reasons for your decision that you are opening the conversation to your in-laws countering with reasons against your reasons. You can say that it's best for your children if they stay at home. Be gracious but firm.
As Michelle M. said, "go, kick off your shoes and enjoy yourself... Have fun!"