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Several of the articles I've read have mentioned confirmation - issued prior to this episode's airing, though they didn't specify - that Brian will be in later episodes this season and next season. So it seems likely that he's going to come back somehow.
As goldomark said, Stewie destroyed his time machine (in the same episode, a few minutes before Brian's untimely demise). He tried to repair it, but
the dealer for one of the parts he needed can't get it for him, since his contact was killed for accidentally drawing a cartoon depicting the Prophet Muhammad.