Final attempt at solving this problem. This time I've decided to separate the 'delete markers' from the 'delete keys' hotkeys, as it proved to be too problematic for users.
The new hotkey for deleting markers is "Shift-XKEY". (or Shift-Delkey)
P.S. I know that 'Shift' is usually used for 'add' operations, but this will have to do for now...
----
Also, rearranged button order in Timeline header a bit to group keyframing buttons together more.