Both universities are on the same level and are reputed state-level Universities with UGC recognition. Only these two are amongst the other 62 universities in India from Harayana, who have autonomy because of their high standards of excellence. 

Kurukshetra University was ranked A+ Grade by NAAC and ranked 8th among state universities in India. 

MDU, on the other hand, has a great infrastructure with new records in sports every year. The university has a comparatively low fee structure and a safe environment for girls. However, in terms of placements and faculty, MDU is still lacking behind.

You should go to Kurukshetra University as it will offer great exposure along with academics.