I'm not sure if this issue is very specific to what I'm working on or if it's a more general problem. Either way, I thought it might be helpful to someone so I'm sharing it:
Setting CACHEMAXFILES to 0 and emptying the cache directory (below) provided a huge increase in speed when deleting objects and saving immediately after. Set at 1, it was taking 13 seconds to delete 5956 objects (all surfaces) and 48 seconds to saveas immediately afterwards. Set at 0, it takes less than 1 second to save those objects and the saveas time was reduced to 25 seconds.
In AutoCAD 2012, before CACHEMAXFILES was introduced, both the DELETE and SAVEAS commands were instantaneous. Please keep in mind that I've only tested this decently large files (20-40 megs) and the only objects in the drawing were surfaces (imported .sat files). This might not be an issue with other object types or smaller files. I have the SAVEAS set to use the ac2013_dwg format.
With CACHEMAXFILES = 0, using ac2013_dwg, save time (after delete) is 25 seconds.
With CACHEMAXFILES = 0, using ac2010_dwg, save time (after delete) is instant.
With CACHEMAXFILES = 1, using ac2013_dwg, delete time is 13 seconds, save time (after delete) is 48 seconds.
With CACHEMAXFILES = 1, using ac2010_dwg, delete time is 13 seconds, save time (after delete) is 48 seconds.