There are no threads in mIRC, just delayed operations on the same thread.
You are really only asking about getting that /timer's switch to keep the exact same code of an alias, that has been made not be called by a timer, just because you are now using a timer.
There are many problems with this suggestion anyway, how do you access the copied environement? Using $nick, no problem, but if you use $1- for example, which is as local as $nick, will $1- be the current parameters passed to the alias or the old $1- definition?
Why do you refuse to pass the information as a parameter to the alias?