Yes, it is OK to file as Married Filing Separately (MFS) when you spouse has a 1099-Misc. But, the type of income is not relevant to deciding between MFS and MFJ. MFS is seldom better and is usually much worse. But the only way to be sure is do test returns both ways.
Try
this tool https://turbotax.intuit.com/tax-tools/calculators/taxcaster/?s=1.
