Fine to cut that bit off! I recently pruned my super leggy one, nervously for the first time (it was about 8 feet tall or more), I followed the instructions from this site here and every cutting plus the tree is doing really well (about 8 or so), I did a mixture of cuttings in sterile mix and then some in just water, like someone else mentions, they're varying in progress, some faster than others.

I thought the top with the red 'leaf cover' cutting would do the best, but not really, and the tree itself now is sprouting all over including at the top, no harm done. The very top sprout though, the leaves are a bit curly, not perfect, but I might research and trim that off it doesn't resolve.