No. Not at all.
Once you capture your clips, select them all at one time in the project pane and tell Premiere Pro to treat the stereo as two mono clips, both linked to the same video clip.
That is not unlinking them, it merely is an extra step to tell Premiere Pro how you want to handle your clips.
One suggestion I have for you is to change the default Sequence settings you use. Change to a stereo master, but with all mono tracks. That way there will be room for your mono tracks in tracks 1 and two instead of all the way at the bottom of the default stereo tracks.
Steven
http://www.stevengotz.com