@JKaechler try M201 X500 Y500. If homing works this way, then you need to set that on homing and create a macro to restore accelerations to their initial values (1000 in your case).
Here's my homex.g (Y is analogous).
M400 ; make sure everything has stopped before we make changes
M915 P0:1 S3 F0 R0 ; configure stall detection
M574 X1 Y1 S3 ; set endstops to use motor stall
M913 X50 Y50 ; reduce motor current to 50% to prevent belts slipping
M201 X500 ; reduce acceleration to avoid false triggering
G91 ; use relative positioning
; X or Y is homed at this point, now home the other axis
G1 S1 X-325 F4000 ; move towards axis minimum
G1 X5 ; move away from home
M400 ; make sure everything has stopped before we reset the motor currents
M913 X100 Y100 ; motor currents back to 100%
G90 ; back to absolute positioning
M574 X1 Y1 S1
M98 Pset_accel.g ; restore acceleration values
set_accel.g restores the acceleration values and has the following contents:
M201 X2000 Y2000 Z100 E9000 ; Accelerations (mm/s^2)