When you copy/paste into excel for sorting, there is a way to eliminate the merged cell problem:
Copy/paste data into excel. After you paste, the pasted data should already be highlighted, or you can highlight the whole sheet or just the cells you want to sort. Either way, the merge & center button should light up indicating that there are merged cells in your selection.
Click the merge & center button and it should unmerge the merged cells
Highlight again as appropriate for your sorting needs and sort
Worked for me. Hope it helps others as well.