You're only talking about a difference of 2 people. In that case, it seems pointless to seat the guests separately. Two people really don't make much of a difference at a table, especially when it's a long table rather than a round one.
Personally, I hate sitting separately from DH when one of us is in a WP. Even if I know tons of other people at the reception, it's hard not to feel like a 3rd wheel, as everybody else is coupled up. And when I'm the one in the WP and DH is sitting somewhere else, I'm constantly worrying whether he's having a good time or whether he ended up sitting with weirdos. Couples, including people in the WP, enjoy themselves more at weddings if they can spend time together.
There are plenty of options other than a traditional head table with dates seated separately:
1) Sit alone at a sweetheart table.
2) Sit with your MOH and BM (and their SOs). Other WP members would be seated at separate tables with their SOs.
3) Sit with your parents.
4) As you suggested, seat the SOs at the head table. In your case, this should work out well, since you're only talking about two people.
If you decide to seat the dates separately, try to seat them with others that they know. If they don't know anybody else at the wedding, try to seat them with people with whom they'd have something in common. It would also be nice if you could enlist a couple chatty guests to befriend them, so they don't feel awkward (especially during the cocktail hour, which is the most awkward part of being at a wedding alone!) At our wedding, I had one friend attending who didn't know anyone else. She did bring a date (which helped with the awkwardness, I'm sure), but I still wanted her to be comfortable and to have a good time, so I seated her with some other friends with similar interests - and I asked a couple of those friends to chat with her and her date. They all ended up having a great time and making new friends. I've also become friends with people I've met at weddings. If I see someone standing alone and looking awkward, I'll chat with him/her and invite them to join my group, if I'm with friends.
For our wedding, we had a traditional head table. I did not want to do it that way (as I mentioned, I don't like being seated separately at weddings and didn't want to subjugate our close friends to that), but DH really wanted to do it that way. It was one of his only requests for the wedding and (for some reason) very important to him, so I conceded and tried to make the best of it. On my side of the WP, we only had one SO. My MOH was my then-15 year old sis, who did not have a boyfriend. Two of my other BMs were single at the time. The other brought her now-husband (can't remember whether they were dating or engaged at the time), but he knew everyone in our mutual group of friends, so where to seat him was a no-brainer. On DH's side, the BM did not bring his wife (that really bothered me, as I was her MOH and DH was his BM, and we took a week off for their wedding. But whatever.) If she had attended, I would have seated her with her ILs, who were also invited. GM #2 was single. GM #3 brought his they're-not-legally-married-and-never-intend-to-but-might-as-well-be girlfriend. They were also part of a group of friends who were invited, so we seated her with the rest of the group. I don't think either SO thought anything of it, as they were both seated with groups of people that they knew well. Not my ideal solution, but as I said, DH really wanted a head table with only WP, so I made the best of it.

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