I just watched a documentary (in Hebrew) on the extremely terrible condition of base food in Israel. After tests on the food, many, many dangerous viruses were found in the food (from multiple different bases), one of which was life threatening. Is it even permitted to eat this food?

Healthy eating is very important, but it's also important to put things in proper perspective. Having spent many years both in the Israeli army and in various yeshivot, I, and probably everyone, can attest to the fact that most yeshiva kitchens have a much less healthy diet, & are considerably less sanitary and are obviously subject to much less outside scrutiny and health-testing than army kitchens. That doesn't mean you shouldn't learn in yeshiva nor eat yeshivah food, but that its cleanliness should be supervised. In addition, journalists, especially in Israel, can generally only publish articles if they reveal something surprising and negative, so you should regulate yourself to critical reading and take what the (generally leftist) press writes with "a grain of salt", especially when dealing with issues of nationalism and religion. That doesn't mean you shouldn't check it out, and correct that which needs improvement, but if you are looking for an excuse not to serve in the IDF, this recent criticism pales in comparison to the super-important mitzva of serving God and the Nation of Israel (in the worst possible case, bring your own food to the army or to the yeshiva!). Always remember that one of the most important rules in halacha, is to keep things in proportion and priority.