If you try smoothing it with a dremel tool, you must make sure the the area you are smoothing is wet, and stays wet while you are working on it. The glass will get too hot if it isn't wet, and there's a good possibility it will break.
A diamond embedded sanding disk would be the best attachment to use (if dremel has one). Diamonds are harder than glass and do a much quicker and smoother job than the grit on the regular dremel sanding attachments (which will not do a very good job).
Also, using the Dremel tool will leave a frosted appearance to the area that you smooth. I don't know if that's the way your professionally repaired pieces look, but, if it isn't, I'd spend the money on having it done right.
I assume those crystal goblets are worth some money. Doing a less then perfect repair on them will decrease their value by quite a bit.
Sue
http://www.freepatternsforstainedglass.com