I've just come across this same issue with a journal I am migrating to OJS. Currently, the only options are to put an explanation on the Journal History page in the About section, or have separate journals.
The Journal History page was a response to this issue arising, see http://pkp.sfu.ca/bugzilla/show_bug.cgi?id=4242
. However, as Judy notes, this leaves OJS reporting erroneous citations and metadata. A quick scan shows a few places where the journal title is incorrect for back issues with different titles:
How to cite RT Tool
Indexing Metadata RT Tool
Article metadata in HTML source, and
Metadata in the OAI-PMH feed
It seems likely that this will lead to incorrectly cited articles. This may cause complications for bibliometrics but I predict that a reader possessing an incorrect citation would find their way to the website of the current incarnation of the journal (i.e., the one named in the reference) and from there find the correct article. Still, it would be nice to see this dealt with in a more comprehensive fashion.