You should use the version 4.0 of the Multiple Site Manager which is compatible with Sitecore 8.1.
The module no longer uses the publish end pipelines to trigger site flush. Instead, there is new event
multisitesmanager:flush:remote to do the job.
So, you can decide when you want to use the flush operation. If you check the checkboxes after creating a site, it is at this moment that the flush operation will trigger.
Note that you need to flush the changes because if you have added a new hostName updated target host name select the check boxes to restart servers. This is required to clear out linkbuilder’s cache (LinkBuilder class is used by sitecore to build site links).
More information can be found here.