This problem has been driving me nuts ever since I updated from 10.8 to 10.11. The older version of Mail was pretty good about replying to the original account, but apparently somewhere along the way it was modified and forgot all about doing that if you use Rules to move the messages out of the account folder.
I believe the culprit is the Preference setting in the Composing tab, "Send new messages from" being set to "Account of selected mailbox"... which means replies from any message you moved out of it's mailbox using Rules will default to going to the first IMAP account in your list. (In my case, a rarely used account I use to manage my Domain Registrations -- making things even more frustrating to me...)
You can make it a bit less onerous by changing that setting to default to your most used account, but that's a bandaid on a gaping wound. What Apple really needs to do is add a setting for "Send replies from" and have it default to "Account the original message was sent to", restoring the old behavior. I've sent them Feedback to that effect, but I recommend anyone else having this issue give the same feedback, so they might eventually listen.