Hi,

It is possible to overwrite the InfoPath template file found in the
SharePoint forms library with out going to the InfoPath form xml file and
clicking file/publish...

But, why do u want to do it only using code? The other way to accomplish
this task is:
1.    Go to Share Point forms library.
2.    In the left side under the “Actions” division click on “Modify settings
and columns”.
3.    Under the “General settings” click on “Edit template” link which comes
under the gray colored quote <template> property.
    Result: It will open the template in the design mode.
4.    Change the template as you want to require (note: if u want to change any
business logic in the code go to tools->programming->Microsoft visual studio
editor, do the changes and save the .js/.vbs file and close it).
5.    And save (mandatory) the template and close it.
6.    Click on “go back to < SharePoint forms library name>”.
7.    And check your template modifications by clicking the fill out  the form.