Saving seeds off healthy plants is always ideal. Quite a few diseases can be seed-borne. However, there are methods to treat seeds if there is a chance they were exposed to disease.
First off, it matters whether the seeds have the diseases only on their surfaces, or whether the pathogens are actually inside the seeds.
There are a lot of ways to remove pathogens from the surfaces of seeds: fermentation, Oxi-Clean, and bleach treatments to name a few.
I've switched over to using Oxi-Clean rather than fermentation to clean my tomato seeds. Both processes will remove surface pathogens, but with Oxi-Clean the seeds are ready to dry in just over 30 minutes and I can skip the fermentation smells. Also, my house tends to be a little warmer than ideal for fermentation and I've lost more than one batch of seeds because they started to germinates inside the ferment in under 48 hours.
But since these treatments (fermenting, Oxi-Clean, chlorine) only take care of surface pathogens, I never save seeds from diseased fruit. I also try to save seeds from the earliest fruit - fruit that set before I saw any signs of disease. That (hopefully) reduces the likelihood that the disease was present in the flower* and could have gotten inside the seeds as they formed.
If you do have infected seeds, the seedlings will probably show disease immediately (cotyledon stage), if they germinate at all. Older plants that get infected probably got the disease from a source other than seeds.
If there is a concern that your seeds might have seed-borne diseases inside:
vegetablemdonline.ppath.cornell.edu/NewsArticles/HotWaterSeedTreatment.html#Table2vegetablemdonline.ppath.cornell.edu/NewsArticles/All_BactSeed.htm (details of the hot water treatment)
A properly done hot water treatment should kill pathogens that are inside the seeds as well as those on the surface. However, note that the hot water treatment has effects on seeds that are similar to aging. Hot water treated seeds can have lower germination and should be planted soon (within a few weeks) after the hot water treatment. Seeds that came from stressed plants, and older seeds, may not be viable after hot water treatment.
So, what does this mean in your case?
Your plant was infected young, but not at germination. So whatever this is probably came from an external source, rather than from the seed.
If you can completely clear the disease (remove all infected foliage and have only clean growth) before flowering, and keep the plant and its neighbors clean through fruit set, I think you can save seeds. Do surface-treat the seeds with bleach, Oxi-Clean, or fermentation.
If the plant keeps an infestation but is mostly healthy, you can save the seeds for your own use and do the hot water treatment a few weeks before planting them. I would not trade the seeds, though.
JMO as a layperson. Good luck!
*Viral diseases are often transmitted to the whole plant through the vascular system and can easily get inside seeds. DON'T save seeds from virus-infected plants. Remove and destroy any virus-infected plants ASAP. Some fungi also travel through the vascular system. Most bacteria don't.