is there any command available in cwcli in which directly I can overwrite Running Config Rather Than Merge On A Cisco Router managed by Ciscoworks.
write2start would be the best way to go as it would absolutely ensure you a clean running config after reload. I didn't mention it because I had assumed you did want a reload.
As mermel said, write2run comes the closest without a reload, but may still leave some residual cruft. Depending on the config it might be sufficient. Else, you can use my import idea, and do the cleaning yourself.