Jonah and Thera were a couple, without a doubt.
Even Kegan disliked them both, claming they both thought they were better than the rest of them. And if I have understood correctly, there were plans to confirm this relationship on screen, but it was dropped later on:

Thera and Jonah were supposed to kiss to confirm that they were in a relationship, but this was dropped because O'Neill had already kissed Carter earlier in the season in "Window of Opportunity". Source: DVD Commentaries
Comment