I have worked on a system to store history item older than item to disk but never succeed to get it working.
here is the source
https://github.com/dufoli/Pinta/tree/history

There were several memory optimizations done in latest version. Can you please install the latest and if the problem with too much consumption of memory still appears, can you please write step-by-step instructions how to reproduce on bug tracker: https://bugs.launchpad.net/pinta

There were also additional memory optimizations in 1.5 development that will be released soon.

There shoud be a possibility to command Pinta to reclaim Undo/History memory when Undo steps are no more needed. That way the memory consumption could be reduced. This kind of "Flatten History" command is used often in memory-critical applications.

Memory usage has been dramatically reduced in 1.5 and 1.6.