We all thought that Wesker was dead after the events portrayed in the first Resident Evil. So while it may appear, rather conclusively this time, that he's finally and forever dead and gone, we'll have to keep our eyes on future installments of the series to find out.
It can be safely assumed he is dead for good, though. Not only was he decapitated by two rockets, after falling in lava, but his remains were destroyed in the rockets explosion. If anything were to remain of him, the lava would have set to burning them away however, so the possibility of him coming back is unlikely.