I think everyone needs to evaluate their own situation and decide on this. In my experience of losing 2 junipers the infection was generalised with all sections of the tree being infected. Not systemic but definitely generalised so cutting out the infection was not possible, because all you would be left with would be the roots. Even if you do cut it out, there could be other areas in the tree which hadn’t reached maturity to for the fruiting bodies to bloom yet and if you cannot control the environment to remove or control the offending partner then it is likely that having shown susceptibility currently it is at risk in the future. If the tree is worth $$$ or has a high level of sentimental value then it would seem wise to put the time in to control it.
Certainly Ryan thinks that rust can be controlled and junipers and at risk deciduous can live side by side. He has produced featured content on the life cycle and control. https://live.bonsaimirai.com/library/video/understanding-rust
The video was summarised in another thread on the forum
After posting the photo of my juniper above with the generalised infection earlier this spring, it was bagged immediately when I found it the day the fungus appeared, the day before it had looked completely normal. Now this weekend I have identified that even though we have had only a few hours of rain in the last 8 weeks, 6 out of 9 of my hawthorns in various stages of development are showing signs of small rust spots on multiple leaves along with the hawthorns on a 6 metre stretch of hedge on the border of my property (I have 50-100 hawthorns in the hedging around my property and half a dozen apple, crabapple trees in my garden and a quite a few other susceptible trees in collection). I am lucky that I am not too fussed about junipers and other than a few nursery stock converts, I see the juniper as being the weak link in the chain and the hawthorns are where the value is to me and I realise the pathogen is endemic to my environment.
This evening I was plucking off infected leave and giving them all a spray with Fungus Fighter. One hawthorn which is particularly early in its development and low value to me was showing a 20-30% infection of foliage, I bagged and threw out. I haven’t decide what to do with the hedge (if anything) as this stretch has at least a few sets of nesting birds, so I can’t cut back the foliage or spray it yet. My XL yamadori hawthorn has quite a large number of leaves showing infection, but it is too big to search through the foliage and cut of the infected leaves so it has had an initial treatment with fungus fighter and I will carefully watch this one.