I have stopped making compost piles and now "compost in place" in my yard/garden. Everything is heavily mulched and I just pull it back, lay down my organic residues and cover back up with the mulch... or, often I treat most as "chop & drop" and literally just throw it down around the plants and let nature do its thing. The whole making a pile and turning (or not) and waiting and then forking into wheelbarrows and/or containers to move around... it's steps that can be eliminated. Even "conventional" farmers spread the manure from their cows out on the fields, they're not making piles and waiting, etc.
I did the compost pile thing for years, but I heard this "in place" way and never looked back. For the small system like ours, I think the compost pile isn't practical. If you had a larger system that's producing a lot of bio-mass, then a pile might not just be an choice, but a necessity. Like so much of this stuff... it depends on your situation.
Regarding the fungus being spread, I would take your tomato plants and put them around other plants that aren't susceptible to that fungus. Use other things around your healthy tomatoes. But, understand, these fungi live in the soil and can't be avoided. I think the best we can do is to help build the diversity in the soil and plant a couple extra tomatoes to help mitigate losses to whatever "pest" may hurt production.
But, hey, that all said, I ain't no expert. I'm just a guy that's been doing this stuff for the past few years and I listen to a big guy in overalls on the interwebs they call a "Duke." Go figure.