I understand that under the tax treaty- I am exempt from US tax for a period of 2 years on my J1 visa, following which I would have to repay

My Q is this: if I leave the county before going beyond this 2 year period, but continue to receive a salary from the University for 6 months (when back in UK), will this also mean necessary tax repayment? Or is it OK?

Any info or help appreciated!

If you earn income from the U.S. unversity while in the U.K for ONE YEAR (not six months), that will be okay. The income is considered to be U.K-sourced and thus subject to U.K. income taxes.

Thanks for your answer. The payment would only be 6 months though, that is fixed (i.e. a 6 month extension on a 2 year job). How does it stand for just 6 months?

If you leave US before 2 years on J1, you are nonresident in US.
Now you work in UK. So any income you receive from US is not taxable in US. You must not be present in US to work.
Also during your stay in US make sure to file nonresident tax return and Form 8843.