Sudhanwa, here is my suggestion. In the flow, sync the lead to SFDC.
After that step, drag in a "Remove from Flow" action with an "Add Choice". In the Add Choice logic, say If Lead Owner is NOT your Marketo user. Make the default choice "do nothing".
Then the next step should be your assignment rules, which will only run if the lead owner is the Marketo user, since if the lead owner was NOT the Marketo user, the 'Remove from Flow' step would have removed them from the flow prior to getting to the assigment step.
I'd also put a 5 minute wait step in between the sync and the remove from flow step.
Make sense? With Marketo, there are usually a number of ways to accomplish the same thing, so maybe someone will come up with another idea.