You want to leave HT enabled even if the AP's ethernet port is only at 100 Mbps because we want to operate the link from the wireless client to the controller/network at the highest rate possible. Disabling HT will cause the wireless link to operate at a peak of no more than 30 Mbps (at 54 Mbps PHY rate). Enabling HT on the other hand could potentially tilt the balance the other way so that the wired link could be slower but it isnt half as bad as it sounds.
It is also important to recall that the numbers associated with 802.11 rates are the sum of both directions (uplink + downlink) because the 802.11 links are half-duplex. Your Ethernet link is probably 100/full-duplex. You can easily construct test cases where the numnerical difference will show up, but for much of the time with real users/traffic, it will be harder to detect that the Ethernet link is operating slower than the wireless link.
Your users will be happier with HT enabled than otherwise.