Hi Peter,
I feel your sadness.
Pseudomonas syringae is the main cause of bacterial canker you are describing. It can manifest itself in other forms too, including a spring bud kill called "dead bud" where the new buds fail to open and simply blacken and die in place.
Before I went 'all in' with Apples, I was focused on Cherries and Peaches. 'Bacterial Blast' and 'Gummosis' caused by Pseudomonas syringae began showing itself in the 2nd year in the orchard. By the end of the 3rd season, it had gotten pretty obvious that most of my trees were infected and after getting some decent peaches harvested in the 4th year, I decided to remove 100% of the trees, including the root balls from the soil.
My trees most likely were infected when I got them from the nursery and the disease simply took some time to show itself.
It is said that Pseudomonas syringae bacteria can be up to 20ft away from a visible infection in seemingly healthy tree tissue, so I wonder if you can truly 'prune' this bacteria out. Once in the tree, this bacteria goes systemic and moves fairly freely within the tissue of the tree and may or may not cause debilitation while some other environmental trigger sets off the cankering, the oozing, the die backs, etc..
Personally, I would not replant into those same holes until I assessed the situation better. In my case, I knew that Apples and Pears were less susceptible to the complete death that can come with Pseudomonas syringae infection -- as the stone fruits are. If you are determined to replant that area into stone fruit, definitely look into rootstocks and cultivars that are proven to be highly resistance to this infection. I understand that this infection is more likely in a sandy soil than a clayey one and that certain nematodes can be a problem in helping to spread the infections. All things to consider.
Be careful of the pruning you do on the stone fruits too and avoid winter pruning and any pruning that is going to be followed by a rain within a week of making your cuts. Lastly, use limb spreading and tie down training when you can and/or make the cuts earlier in your summer training (when possible) when the branching has a smaller diameter, to help the tree to heal faster.
Here in California, UC Davis has done some extensive research on Pseudomonas syringae and the infections it creates and methods for dealing with it.
Here is a link to one of their IPM sites that is dealing with PS.
I found my cherries to be a little more susceptible to the bacterial cankering than my peaches, but most cherries and peaches are at risk and the methods for addressing the infection are similar.
Here is a link to a nice write up on Bacterial Canker Management.
The
PNW Plant Disease Management Handbook has a really good overview document on PS too
Mechanical damage, susceptible times, seems to be high on the list of likely infection portals for this pathogen. Painting your young tree trunks to avoid winter injury and trunk splitting makes sense and is a good practice, in general. When I plant a young tree, I have now begun just painting the entire tree vs just the trunk with a 50/50 interior latex paint mixture -- as all of that young exposed tissue is subject to scald before the canopy fills out in the years to follow. Hail and high wind damage can also be just the opportunity needed for an infection to get a foothold into a tree too. Also, PS is ubiquitous in most of our orchard environments, and infection can take off as a result of high bacterial counts in plants growing within the drip line, and up against, your young trees. Keep that competition at bay for the general health of your young trees and to keep those potential infection sources from being right up against your young trees too.
In my opinion, if you are seeing the rust colored gummy ooze coming from trunk, your trees are in decline and will likely be dead within a few years. It is a source of infection, even if the jury is out on how well the gummy ooze travels from one spot to another. When we removed our trees, we had them hauled to a dump as burning was not going to be an option until the rainy season which was still several months away at that point. If you wish to burn them; you can.
Good luck!
Gopher Hill ApplesZone 8 in California