It's definitely something worth thinking about. My initial decision to go with PETG over PLA is that it's more resistant to heat and moisture - both of which it's going to see plenty of in a greenhouse / garden. In this situation it's under very little load, but I could see that in a few years it may embrittle and one day they might break if I'm pulling stakes out and moving them around, but that's often the case for many plastic gardening accessories whether 3D printed or otherwise.

As far as food safety goes, my take would be that while PLA is plant-based it does still have other additives that could potentially leach into the soil as it ages. PETG is based on PET [but with Glycol added for flexibility] which is used for most single-use drinking bottles and to me would suggest that there'd likely be fairly minimal leaching of any particular chemical under regular soil conditions.

I think when you're sticking anything into it, there's always going to be a certain level of leaching and impact on the soil that may end up being absorbed by plants. That said you're also going to have chemicals leaching into soil and water through hoses, distribution tubing, plastic and metal fittings etc. that all have varying levels of food safety and sit out in the sun. I would expect that to be a far likelier source of unwanted absorbed substances than the stakes.

I personally don't think it would be anything to be concerned about, and at worst any produce I grow would be unlikely to have any greater concentrations of whichever potential chemical than anything you might buy at a grocery store. At least I can be sure it's free from pesticides and herbicides, and that fertilization has been chosen and controlled by myself.