Option 1: You can just not include the -m MSC_map.txt option to make_otu_table.py. QIIME doesn't ever use the sample metadata from the biom file, so there really isn't any benefit to including it. Any time the sample metadata is used by QIIME, you're required to pass the sample metadata mapping file. In this case, your new command would look like:
make_otu_table.py -i 3_usearch_qf_results/combined_seqs_otus.txt -t MSC/3_usearch_qf_results/uclust_assigned_taxonomy/rep_set1_tax_assignments.txt -o 3_usearch_qf_results/MSC_otu1.biom
Option 2: If there is a specific reason why you want to include the sample metadata in the biom file, you can try uninstalling h5py. This will cause QIIME to fallback to writing BIOM files in the JSON format, and should get you around this error.
Can you follow up here to let us know if one of these two options ends up working for you? It'll be helpful for us and other users to have that information.