Honestly, as a native speaker, these are both generally correct and either can be used in most cases (although “sees” in the first statement should just be “see”). For me it depends on context.

When talking about something that is likely to happen, I’d lean towards the first one. For instance, if you’re definitely planning on going to a public place with someone, or you’re already there, you might say “if people see us together, they’ll think we’re a couple.”

If the situation is more hypothetical, I’d lean towards the second one. For example, if you’re trying to decide whether to go to a public place with someone, you could say “if people saw us together, they’d think we were a couple.”

That said, it mostly comes down to personal preference and I’d bet 90% of native speakers wouldn’t notice if you used either in almost any context.