As discussed in the several studies on name collisions published to date, determining which queries are at risk, and thus how to mitigate the risk, requires qualitative analysis (New gTLD Security and Stability Considerations; New gTLD Security, Stability, Resiliency Update: Exploratory Consumer Impact Analysis; Name Collisions in the DNS). Blocking a second level domain (SLD) simply on the basis that it was queried for in a past sample set runs a significant risk of false positives. SLDs that could have been delegated safely may be excluded on quantitative evidence alone, limiting the value of the new gTLD until the status of the SLD can be proven otherwise.
Similarly, not blocking an SLD on the basis that it was not queried for in a past sample set runs a comparable risk of false negatives.
A better way to deal with the risk is to treat not the symptoms but the underlying problem: that queries are being made by installed systems (or internal certificates are being employed by them) under the assumption that certain gTLDs won’t be delegated.