There is no Guvnor/KIE to manipulate the repository since it is GIT-based and there are a myriad of client libraries that can be used instead.
I am a little confused by your comments "We need to push our changes on run time into guvnor repository programatically" and "Note : We are not using drools workbench UI to checkin our changes". What do you use the workbench repository for? Your comments imply you don't need the workbench webapp at all - in which case why try to re-use it's repository?
@Alexandre, @Kris,
What have you tried (and been successful with) for Eclipse->KIE-WB Repository connections?
Cheers,
Mike