I do not analyze the concept, as it is not very clear to me what you are trying to accomplish here, and do not know the dataset, but regarding the problem with the covariance matrix:
The most obvious solution for data, where you need a covariance matrix and its determinant, and from numerical reasons it is not feasible is to use some kind of dimensionality reduction technique in order to capture the most informative dimensions and simply discard the rest. One such method is Principal Component Analysis (PCA), which applied to your data and truncated after for example 5-20 dimensions would yield the reduced covariance matrix with non-zero determinant.
PS. It may be a good idea to post this question on Cross Validated