Hi Laskhmanreddy,
As you already know that it's a standard behavior because that field occupy the whole row hence it will activate/deactivate the checkbox even if you click on the blank space (not on the label) on that particular cell(row), it will behave in same manner.
If you want this not to happen only for a particular custom checkbox then you can try creating the checkbox in .htm file for that view directly using thtmlb tags and it should work as expected.
IMHO it's better to convince the customer by explaining the standard system behavior than ending up with these kind of unnecessary development which might give them the option to ask for similar stuff in future thus ended up with issue during upgrade.
Well I have one more idea in mind if you still need that 
Rgds,
Shobhit