Yes, that really happens all the time, if by "every level" you just mean "both the upper and lower levels of the transition that has energy Ei". It almost sounds like you are asking if the atom is as likely to be found in any possible level for that atom, and that only happens when all the energies are << kT, including the ionization energy. When that's true, there's very little chance of finding that atom in the first place-- it will be ionized.
If your question is just about the upper and lower levels of some particular transition in an atom that takes much more energy than that to ionize, then it happens all the time that the atom will be almost equally likely to be in the upper or lower level. For example, much of the radio spectrum deals with observing transitions whose energies are much less than kT, and as a result, the lower and upper level populations are very close, and this produces a great deal of stimulated emission and completely alters the nature of the radio brightness.
By the way, some imagine that when Ei << kT, we should expect the upper level population to be greater than the lower, but you are correct that this is not the case.