You can but that really does not address your problem. Time Machine will delete old updates when the Time machine disk is full. If you delete information from the internal HDD and Time machine deletes it from the Time Machine drive, that data is gone.
If you need room on your internal HDD, delete data that you no longer need or transfer that data to a separate external HDD (not the Time Machine HDD). Time Machine is a backup medium, not a storage medium.