Sorry to say that there is probably no workaround to this.
We tested the subversion integration ourselfes and there are two main problems concerning your behaviour:
The subversion integration was obviously added as an afterthought to a svn integration which does not really match svn principles. When doing checkin/checkout the package is performing a tremendous overhead of svn access, which leads to the bad performance.
The subversion client is not able to separate multiple user properly when accessing the same IS. Even configuraing the user mapping in the vcs package homepage does not help. So you may even encoutner assets you checked out locked by another user id.
My best experiences so far are in using an indepentend SVN client and adding some custom made scripts for automation.
You also need to be aware that all .svn directories should be removed before using deployer, letting those in the deployed packages leads to problems in the deployment process.
Overall we are all waiting for a proper svn implementation for webMethods. There is a request on Brainstorm, perhaps you like to add your voting there.
#webMethods#Integration-Server-and-ESB