If I’m reading your story correctly, and the objective is to simply get out from under this mess, then why not simply ask your nominee (the real estate agent) to sell the property again, to someone else? I don’t see any point, or advantage to encumber the Hak Milik (land deed) with a Hak Pakai, as that will only make the property less desirable.
In the “old days” when using a nominee was more or less overlooked by the government (although essentially still in violation of the law as it is now being interpreted), the Indonesian nominee would complete three documents, a loan agreement, an irrevocable power of attorney, and a right of use lease.
The following is as good as any description of that in more detail:
Your partner may just as well be better off proceeding on that basis (as described on that web site) and keep his fingers crossed.
To your advantage, but likely only temporarily, the government is concentrating more on Bali and Lombok than anywhere else right now.
The biggest risk, as I see it right now, is that your real estate agent/nominee is trustworthy.