It's not clear if head of household would be allowed. Incarceration may count as a "temporary absence" that would not fit the definition of "lived apart for the last half of the year."
Even if HOH would be allowed, married filing jointly will usually result in lower taxes, especially considering that your spouse will not have much income this year. Joint filing is allowed as long as you both agree. If you visit your spouse, there is an IRS POA form for taxes only that you could have him sign, just to cover your bases. But you would not need it if you plan to e-file, it would just be a backup in case there was a dispute later.
https://www.irs.gov/forms-pubs/about-form-2848
