Slow Cooker & Fat - Blend it back in?
If you wish to continue down the road of a singular dish I would recommend the emulsifier. Incorporating the fat through blending it with some of the liquid in a side pan or pot with ground mustard would be easiest and most complete. You should be able to continue cooking without further separation.

However, if you are cooking the dish too hot you may be forcing some of the fat from the meat or otherwise loosing it from too much agitation and you will want to make any adjustments necessary.