http://hebrewbooks.org/pdfpager.aspx?req=14061&st=&pgnum=358 (Mesech Chochmoh – referring to the obligation to build another 3 Orei Miklat when Moshiach comes. This seems to imply that people will still be killing bshogeg and need refuge).
There is also a famous (and often misquoted) Gemara in Niddah (55?) where R’ Yosef says מצות בטילות לעתיד לבא – the mitzvos will become obsolete in the Future. This gemara is subject to numerous arguments in the commentaries – mainly, what exactly does בטלות mean, and which period of time is this referring to. Of course, if you were to take this gemara literally (as many Rishonim do), then you have an answer to your question.