Possible fungal disease and mulch. Two part question
 

Last week, I noticed that the lower leaves of some of my tomato plants were turning yellow. I haven't pinpointed the exact issue, but suspect either early blight or Verticillium Wilt and will be bringing a sample to a local garden center for confirmation.

We've had an extreme amount of rain this year (I think only 3 days in May were dry and maybe 6 in June), so things out there have been very wet, so the potential for fungal issues has been high.

Due to a variety of reasons, I didn't mulch the bed, but I bought some mulch yesterday and now I have questions.

My plan had been to mulch the bed, then till and/or leave the mulch there over the winter to help amend the bed, since I'm dealing with clay soil. However, now I'm reading that tilling in mulch is a bad idea, because it ties up nutrients until it breaks down.

1) Is it a mistake to use mulch in this manner? The mulch in question has not been aged.

2) Am I creating a good habitat for whatever fungus that's attacking my plants if I use mulch to begin with? My primary objective is to try and limit splashback, but I also don't want to create an ideal environment for the spores.

3) Would it be best to use the mulch, then remove and dispose of it after the season because of my concerns in question 2?

What kind of mulch?
Whatever it is, don't till it in.

Foliar fungal pathogen spores can not become vegetative and reproduce on dead organic matter, they need live tissue to become active. So your mulch and soil can harbor spores, but that's it. If those spores can get splashed up on the leaves then they can infect the leaves and reproduce.
Verticillium Wilt is caused by a soil born pathogen that infects through the roots. Mulch won't affect it one way or another.

Thanks, RayR. Now that I've had a chance to look at the plants a bit closer, I think there are a couple of things going on. Only a couple of plants so far have the yellowing leaves and they are next to each other. I also found some lower leaves on some plants a bit further away that were full of pinholes. So today, my focus is going to be doing some cleanup and taking pics.

As far as the mulch goes, it was the cheapest they had. It has no artificial color and is made out of tree limbs.