Hi Santosh,
As long as having those timesheets submitted for users on a long leave, I don't see that as a problem since the timesheet will still follow your normal approval process.
The hardest part will be to determine who to run that process for. You would not be able to use an Autostart process since there is a good chance nothing will change. You might want to create an attribute with the different types of leave that would trigger this process (i.e. maternity, vacation, fmla, ...) on the Resource object. Then you could create a gel script process that uses a database query to search for all users with these values set in that attribute. You could then use a gel script to xog in the timesheet with the values you want and the submitted status.
This is a very rough outline. But it could certainly be done. If you don't have the in-house knowledge to do this and this process is important to you, you could engage CA Services or a partner to write this process for you.
I hope this helps.
Jeanne