Is there any semantic web reasoner (e.g. Pellet) that accepts rules (SWRL) on the fly ? or rules must be hard coded before starting the reasoner
It is unclear what you mean by "on the fly". You can edit a reasoner's rule base, so it is not something you need to set in stone from the outset. But the reasoner will need to perform some book keeping if you add new rules, or any other axioms, before it can be used to answer queries. There's no way around that.