Certifying an engine and creating the campaigning and aftersales support for it are probably harder than building an engine, in a market like very light general aviation. Firstly, there are no current Turkish builders that would use it. If Baykar sees a possibility there, it will try to enter the American and German markets, as there are no other markets. That means FAA and EASA certification. That's a multi year process, but it's doable.
Then, Baykar would need to advertise the engine to builders, so that they would choose it over more readily available options. Builders in this market are all small time builders, so they want a cheap, reliable engine with aftersale support readily available, so that they won't have to worry about the engine. Entering that market is hard, but it's again doable.
Next hurdle is the aftersale support with maintainers on site, that would require distributors in multiple cities. Which is again doable but expensive.
All things considered, it's an entirely business choice from Baykar and its partners whether they enter GA or not, I don't really think it's a defence issue at all. We never had any actual problems with procuring Rotax engines until now, and we won't have any problems with it in the future. They grow on trees. Anyone can start a simple LLC and buy 20 crates of them for anything.