Yeah, with pure dollars and cents Job #2 is better.Total gross compensation at Job #1 is $27,445 and change (if he works 40 hours a week, 52 weeks a year, and maxes out his 401(k) benefit). Job #2 is almost $12k more per year. After taxes, you're looking at ~$700 extra per month, which is nothing to sneeze at.
The benefit of an employer 401(k) [other than the match, which doesn't make up enough ground in this situation] is that you have a ceiling of $18k to save in a retirement vehicle. But with gross wages of $27040/year (if he works 40 hours a week, 52 weeks a year), it's unlikely you'll hit that anyway (unless your job completely supports your family, and basically all of his wages are for saving). He can save $5500 in a tIRA with the same tax benefits (or $5500 in a Roth IRA, if the work option for Job #1 would have been a Roth 401(k)).
I agree with you; the commutes are negligible. There may be some psychological benefit to working from home/with other people on location, depending on his preferences. But even if he really loves working from home, I think it would be hard for me to say that's worth $12k/year.
The one thing I'd consider is how stable your job and health insurance is. Do you think it's at all likely that you would lose either your job or your benefits, meaning it would be valuable for him to have a job where he can choose to pay for insurance? If it's possible, but unlikely, I'd take the risk of having the extra money. If it's likely or something you're really worried about, you can think whether you want to essentially pay $12k a year for a health insurance backup. (I probably wouldn't).