I'm not certain, but I don't think you can adjust the merkle root without needing to recompute the midstate as well?
You're right, the merkle root spans both SHA-256 (512-bit) blocks, so you must recalc the entire SHA-256 from scratch.
| Byte len | Byte pos | Bit pos | SHA block | Field |
| 4 | 0 | 0 | 1 | version |
| 32 | 4 | 32 | 1 | previous block header hash |
| 32 | 36 | 288 | 1-2 | merkle roothash |
| 4 | 68 | 544 | 2 | time |
| 4 | 72 | 576 | 2 | nBits |
| 4 | 76 | 608 | 2 | nonce |
| 80 | 640 | | (end) |