I have the same issue with one of my servers. The original use of the server was to host a datawarehouse generated from our mainframe.
However, overtime I've been asked to host several vendor applications which do not have the same collation.
I find it better to simply run an alter after the application insatll has setup the database. Or if the database is created from scratch, just use the drop down list and pick the desired collation.
ALTER DATABASE database
COLLATE < collation_name >
"If it ain't broke....."