Although the final upgrade to empowered is only a small upgrade in rf/t, the empowered oil lasts much longer so the energy per fuel is nearly doubled. Crystallized oil gives 560,000 rf/bucket while empowered oil gives 960,000 rf/bucket in an AA oil generator.
Empowering the canola seed seems to take 3,960 rf. Each cloche takes just 8 rf/t and takes about 12 seconds (240 ticks) with bonemeal or 16 seconds without to produce 1 seed and 3 canola (4 seeds if converted). Crystallizing the seed is 2,000 rf each with 1,000 rf per atomic re constructor operation.
Even by the least efficient method where you convert no canola to seeds, the cost would be 16,763 rf to convert crystallized oil to empowered oil. With more efficient methods you could get that down to under 8,000 rf per conversion. This leaves you with at least 380,000 rf profit.
TL;DR: Empowered oil is still very profitable despite the nerf. Just make more oil generators to compensate?