Thank you for your post into the forum and sorry that SQL Compare maybe the cause to a locking issue.
Comparing from a snapshot file maybe a solution for you to try. You still may experience a locking situation during the period that the snapshot file is being generated. However the creation of the snapshot file is generally does not produce a huge overhead.
Are you able to provide further details on the locking issue you are experiencing? Is the server very busy at the time the comparison takes place?
Alternatively, there is a little utility that will generate a SQL Compare Snapshot file for you called SQL Snapper which is available as a free download HERE
There is not a feature within SQL Compare for management of snapshot files. I can submit a feature request on your behalf to request this be added in a future version of the product?