Bible commands are limited by their contexts. We cannot, for example, apply I Cor 7:3 to the assembly for it violates other principles (e.g. Eph 5:12). The principle that you apply from II Jn 9 acts in the same way that a generic application of I Cor 7:3 does in that it contradicts other Bible passages. The principle that some draw from II Jn 9 causes a person to be lost for the most trivial violation of God’s law. If you sit down in your car and don’t put on your seat belt, you are lost. If you park in a handicapped parking spot, you are going to hell. If you go 1 mile per hour over the speed limit, even if you didn’t intend to, you are lost. The use made of II Jn 9 contradicts I Jn 1:7 and Rom 14 and serves as the foundation for the perfectionist doctrine. That is, if you do not KNOW and KEEP God’s law perfectly, then you are lost unless and until you repent and pray. That is the use that is commonly made of II Jn 9, and it is what you did with it. However, II Jn 9 is not a generic catch-all to use when we can’t find anything else to condemn something.
If we want to use a text in context to deal with eating in the church building, then I Pet 4:11 is much better than II Jn 9. However, the context of II Jn 9 describes a very egregious error where men were claiming that Jesus did not actually come in the flesh and therefore (though these teachers did not say this) could not have actually been a sacrifice for sin. The Gnostic teaching about Christ was a horrible doctrine because it leaves man hopelessly lost, and John said people holding that doctrine did not have God. That is hardly comparable to some person who sins ignorantly or makes some small infraction of God’s law (Jn 19:11, Mt 5:19).
God’s judgments are just (Ps 119:75), but our use of II Jn 9 does away with the justice of God. Our use of II Jn 9 gives God no choice but to send any kind of transgressors directly to hell. That is not correct (Rom 9:15, Rom 14:4), therefore our use of II Jn 9 is not correct. II Jn 9 only makes sense limited to the context of just what John said–people who denied that Jesus came in the flesh.
The view that II Jn 9 applies to everything we do wrong springs from an interpretation of the verse that ignores its context and understands the text to refer to what Jesus taught rather than the doctrine about Jesus. The context clearly means the teaching about Jesus (cp II Jn 1:7), therefore we cannot use II Jn 9 as a generic condemnation of everything that someone might do wrong.