Why shouldn't any of them been shot?
Both were confirmations to the highest level of office in their respective branch of government and both were staged by political opponents protesting and admittedly attempting to block an "unjust" transfer of power.
If "peaceful protest" vs "riotous coup" can hinge on the fact that your ideological allies could only have been there to "righteously have their voices heard" but ideological opponents must be there as "murderous usurpers", then your sympathetic reasoning might be better described as paranoid delusional projections.
Let's remember that it was Eric Holder and Bill Clinton who pardoned a woman who literally bombed the capital building.
Another one of those groups broke into the capitol building, stole things, destroyed things, fought with guards, smeared poop on the walls, audibly shouting about looking for specific senators. and at least one person has been found guilty of carrying a gun. Multiple people found to have discussed killing the senators.
Your final reference (I'm assuming to the weathermen) is a much more apt comparison than the other protest you're discussing.
Supposing they instead entered the room, it is probable to me that they would have been immediately shot. I doubt the rioters could have taken the room but who knows. In any case
* I think the rioters would have killed some democratic leaders if given the opportunity
* I think more gunshots would have occurred if the rioters went a different direction by chance
* I think this is way, way too far already in terms of what is remotely ok.