I say you should stop trusting them in your systems ASAP. I’m just going to leave this here:
I’m really glad all of my websites now use Let’s Encrypt. At the same time, I think this means that Let’s Encrypt now is a “monopoly” on the free certificates market – which, all things taken into account, is probably a good thing, as they seem to be way superior to the alternatives both in technical and ethical terms. My only problem with this is the “centralization” that arises: no matter how well Let’s Encrypt is managed, all it will take is the compromise of that single CA to cause major havoc.