like an app won't delete from applications folder with mobile finder.....

"rm" is the command to use

So I would assume you'd want to do rm /path/to/application

or

rm -rf /path/to/application

Where "/path/to/application is the FULL path to the app you want to remove.

Safer method might be to use SCP (WinSCP if using Windows) to connect and then delete the folder using that.