I think the reason this was disabled by default is privacy - a user may want to appear as away eg. if they are talking privately with someone else or working on a script on a private channel, and so on.
Privacy conscious users generally know how to check the boxes that they need. While most beginners might not even know there is an option they can tick that lets them cancel the away status automatically.
One possible solution could be: if you message someone while they are away and they reply, mIRC could temporarily hide subsequent away messages eg. for the next five/ten minutes.
Five to ten minues sounds more reasonable than originally proposed 2 hours. Or perhaps an option to set "Ignore subsequent away messages for [xx] minutes".
