I'm with A.X. on that. Get that glass out, clean the channel, take care of any rust and re-install it. You won't have to worry about it any more. Warning though, if it's a 2nd gen, it's probably got the urethane sealant rather than the ribbon and it's tough to get out.
My glass guy told me that one of the worst things people do is put RTV or silicone sealant around a window. Said it never really seals water-tight and merely serves to trap water, compounding the rust problem.
If it was my car, I'd take it to the glass shop and let them do a remove and replace. They'll treat the channel with a rust preventative primer and re-install it with urethane. You'll probably never have to screw with it again.