IANAL, but the difference is that in this case, QI came into being as a (very narrow) reading of federal law (ยง1983), which congress can amend easily. The Loving case was decided on an interpretation of the constitution, which as you say, is much harder to amend.
This is nitpicking by you, in my opinion. There are of course levels of authority between the judiciary and the legislature. Nevertheless, Congress can always overrule SCOTUS, it just depends what level of law they need to pass. A constitutional amendment is lawmaking.
Wow, that's wrong...
Take Loving v Virginia: there, the court ruled that interracial marriages must be governed by the same rules as all other marriage.
No law of Congress can overturn that ruling. Only amending the constitution or the court itself have that (theoretical) power.