I use legato notes a lot for 303 style sequences, I control the legato by using the EDIT mode and selecting a step (originally recorded in realtime and first doing rough length adjustment by choosing the length in the matrix, then doing fine adjustment by using the LEN encoder.
Could you just change the length of the offending notes easily with this method rather than a dedicated "non-legato" mode? How many notes are you having to change?
Maybe such a specific edit function would be too obscure? I would wish for the converse function then, "make legato"! 
Also the handling of legato notes is usually determined by the sound module receiving the notes, whether it will retrigger the amplifier envelopes, or if the synth is monophonic or in mono mode, maybe you can avoid the whole issue?
cheers
ripe