If there isn't any spa suction line, then there isn't any way to heat only the spa without also heating the pool.
That plumbing is a mess. Replacing it all would be a good idea. However, you should find out as much as possible about what each pipe does before you take it out. My suspicion is that there is a spa suction line somewhere. If there is, it simply isn't plumbed to the suction side of the pump.