First and foremost, I'm drawing my comic for myself, so even though I hate disappointing people, my story is too important to me for me to change it based on what other people want. The only reason where I can think changing your story based on reader's reactions would be right is if the response to something is overwhelming negative, like the story takes a turn the readers weren't expecting and the majority seem to feel it wasn't a good move (and it isn't something that's going to be cleared up later). But even so, if you decide to change something like this, you'll want to run it by trusted friends/family first!
I like this! I think as long as it doesn't derail the story you have planned, giving a popular side character a bigger role than you intended can be a good change. And I'm sure it feels good to know your readers loved a character more than you were expecting them to!
It is worth noting that if someone gives you a suggestion and you end up using it in your comic, you could possibly run into legal problems for taking their idea. There's probably a very small chance of this happening, but it's a good thing to keep in mind just in case! (authors sometimes have policies about not reading fanfic of their work for this very reason) (and of course this doesn't apply to friends who are helping you brainstorm for your story or anything like that)
Anyway, I think the main thing to keep in mind is that no matter how good your comic is, not everyone is going to like it and that's okay. It's disheartening when someone expresses that they don't like something, but just remember the people who do like it! And if you changed things then maybe they'd be upset. Just tell the story you want to tell, if you're passionate about it then others probably will be too.