Merging is non-trivial.
If both sites started with auto-increment at 1 you'll have a lot of collisions for topic/post IDs. You'll have to consolidate accounts, after you've done that there will be quite a few changes in the DB when it comes to user IDs.
Nothing is impossible, but it's a lot of work for a situation that's fairly unique.
If you first want to test Flarum and keep that content after a conversion a bit of planning makes everything much easier. I.e. make sure the User IDs are the same between the two systems and make sure that topic/post IDs of the Flarum setup start at IDs quite a bit higher than MAX(topic_id) and MAX(post_id) of your old system. If you do that merging should be fairly doable.
Regarding the API of SQL question; I would prefer SQL by a very large margin. The API route is a no-go if you have a larger database (I.e. more than a few hundred thousand posts).
@jacko; what did you end up doing? Have you converted/merged? Or are you still waiting for stable?