When leveling hotend always slams into bed? If the hot-end is at ~0 on the Z axis and I go to level it, as it approaches X = 0 it begins scraping along the bed, then when moving back to probe the center of the bed (after homing X to 0) it will scrape the bed again.

I want to add a glass plate but am worried this aggressive homing will smash the glass. How can I fix it? The printer auto-levels and runs Marlin.
I realised the simplest fix for this shortly after posting the question. In either your slicer or your printer controller (I use octoprint, so I added this there) add to the starting G-code something to lift the head so that it is above the point it is scraping across.

For example, change your starting G-code from something like:

G28 ;Home all axis
G29 ;probe bed


To

G91 ;Set to relative positioning
G0 Z10 ;move head up by 10mm

G28 ;Home all axis
G29 ;probe bed


(obviously remove G29 if you do not have a probe)

10mm should be more than enough to lift by unless you have something seriously wrong, but you can adjust the figure as needed.