Elena--
I have attached some slides from one of my classes--maybe they will help to explain the basic concept of proportionality constraints. These slides present this at the level of observed variables loading on a factor, but the first-order / second order situation is entirely analogous.
It is a common misunderstanding that the factor model is all about strong covariances, when it is really about a pattern of covariances. In exploratory factor analysis, where there may be several factors linked to a given observed variable, the pattern is obscured--not so obvious to see.
Your second order factor model implies proportional covariances among not just the three first order factors but between them and any "downstream" variable that is directly or indirectly dependent on the second order factor (a "descendent," in the language of causal inference) and does not have any other relation with the first order factors. So it could be that the real violation of proportionality has to do with relations between the first order factors and some downstream variable.
It also could be that the real problem is the assumption of linear relations between first order and second order. Maybe the correct relation is exponential or quadratic.
Or maybe you want to capture the failure of proportionality by creating another second order factor. Even with only 3 first order factors, you might be able to estimate such a model if you fix the loadings of two first order factors on this one to equality and you make this second order uncorrelated with the other second order.
What is the "best" thing to do? That depends on your goals and your prior knowledge. If your goal is to publish, then look at practice in the venues where you want to publish. If you have prior information about some of these variables, then you might favor a model where those variables behave like they are supposed to. Without specific goals and without prior knowledge it is hard to say what is best. Sorry.