If it was mine I would have the scratches removed. Regarding 'allowed', who knows what has happened to antique weights in the past 150 years - many may have been repolished, perhaps more than once - and some even in the factory at the time they were made. I think what is unattractive to collectors is when the profile gets changed significantly, so that the paperweight ends up as a flat pebble, or the change to the profile makes the optical properties different, and so the outer canes 'vanish off the edge'. Removing shallow scratches should not affect either of those aspects.
Bruises are a more difficult issue than scratches, as much more glass has to be removed. But there is always a risk if you have a paperweight restored, even just to remove fine scratches: stresses within the glass can cause them to fracture into several pieces. That is a smaller risk with lead glass antique weights than, say, early Paul Ysart weights, which were not always annealed effectively.