I have been working on this for several hours. SONAR is not broken. It is working just as it has since at least V 8.5. A MIDI clip is always going to follow the tempo map (a quarter note is a quarter note regardless of tempo).
It may be easier to make this type of edit in another program (I would not know), but this is how to do it in SONAR.
First make sure that "selection after single split" is set to "right portion" in Preferences.
1. Select the clip(s) you want to work with and set the now time at the first note of the clip. Hit "Tab" which will move the cursor to the next note. Hit "S" which will split the clip with the right portion selected. Tab-S your way to the end of the clip.
2. Select all of the resulting clips. In the Inspector, Cntrl-Click (quick group) the Time Base to "Absolute" and Lock to "Pos Only".
3. Make your tempo change(s).
4. Re-select the clips (it is likely that some will move out of the selection range after the tempo change). Open the PRV and adjust the note durations as needed. Some may need to be adjusted individually.
I hope this is helpful. Good luck.