In that case, you really do need to align Cubase’s tempo to your unchanged MIDI Track (presuming that, “musically”, the notes are intended to be quarter-notes (or multiples) exactly on beat starts?).
And, looking at your screenshot, I think the best method in this case is the TimeWarp Tool (and using the key Editor’s “Snap to Events”, rather than to “Grid” Snap setting). Work from left to right, dragging the barlines in the Key Editor until they Snap to the start of the desired note (or, if the notes are intended to be 8th-notes rather than quarter, drag the1st and 3rd beat lines of the grid ).
Then all you have to do is change “Snap” back to “Grid”, and, with the Scissors tool, split each note on the 3rd beat of each bar (or whatever is the half-way point of the note). The whole thing shouldn’t take you much more than twice the realtime speed of the music .
This (having done the tempo map) also then gives you the possibility of syncing other MIDi stuff to it, adding tempo-synced delays etc. .