My, my, again. Take a few deep breaths before reading further.
My take of it is that whether Federal troops were coming to help quell the riots or passing through Baltimore, in either case there would have been more riots. At least that apparently is what the mayor and governor feared. They thought they were sitting on a powder keg. Earlier they had worked to keep the pending arrival of the Massachusetts troops a secret from the populace knowing there would be problems, but it didn't work -- the townspeople found out and a riot ensued. In the minds of the mayor and governor, blocking further access of the troops to the city saved people's lives on both sides.
Also, you might be interested in the following site: Maryland History. According to this site, the mayor threatened the citizens with gun in hand during one of the confrontations with troops and peace resumed for a while. The mayor then met with Lincoln and Lincoln agreed that Northern troops would not pass through Baltimore. Routes were found around Baltimore.
Feel better?
No, the website is unattributed. Was that someone's high school term paper you referenced?
While I believe that Maryland Governor Hicks was ultimately a friend of the Union, his actions in the weeks immediately after the start of the Civil War are suspect.