Milorganite isn't organic. It's human waste products. It is not recommended for food crops. Only for lawns.

You'll always have rain and sun and damage.

>> is there any use in even keeping them in the ground?

Yep. Definitely. See what happens. Most of your damage is on non-edible foliage so unless those leaves are ruined to the point of not supporting the plants, there's no "practical" damage.

You could also push some insurance seeds into the dirt right next to the plants that you expect to not make it. You could spread a hefty layer of composted -something- all over and cover that with straw, leaves, or some other airy mulch to add some soil heat protection and even out your soil moisture a tad. Then just wait a bit.

So its just damage from the rain? Not any mineral defiency?

Milorganite most certainly IS organic if not OMRI approved. And it can be used on any type of plant including vegetables.

The term "human waste" is a bit of a misnomer. Biosolids are a very different kettle of fish than is sewage or human waste and while they may very well be the origins, it is unrecognizable both in appearance and smell than what one commonly thinks of as sewage. Generally, the argument about Milorganite revolves around the percentage of heavy metals it contains, not that it is a biosolid. Biosolids are generally well respected as an organic fertilizer provided one does not carry a lot of squeamish preconceived thoughts about it.

As noted, weather is impossible to predict accurately or to even guard against so we are all pretty much in they same boat in that regard. Insects are another matter. They are difficult to be very proactive with aside from protecting the crops typically damaged with row cover or similar products or companioning with insect deterring plants. Controlling other insect problems requires accurate identification of the insect pests then following an appropriate course of treatment directed at controlling THAT insect. Thuricide (Bt) is a perfectly acceptable organic control but only for certain types of leaf eating larvae - it will not control any other insect pest.

As best as I can tell from your photos it looks like flea beetles may be an issue. The row covers are strongly suggested for this problem. And I agree that unless the insects are damaging the edible portion of the crop or seriously jeopardizing plant health, there may not be a major need to treat at all. Much insect damage is cosmetic only in character.

How was that soil pH determined? A good reliable soil test or a home test kit that often gives unreliable results If the soil pH is that low many nutrients may not be available to the plants, what I see does indicate nutrient deficiencies.
How much organic matter is in that soil?
How much life, earthworms, are active in that soil?
What does the soil smell like?
How well does that soil drain?

One sign of organic plot of plants is lots of bugs!!

Your soil looks a bit dry though -- enough to show cracks like that.