Ok, I'll confess that I'm not sure what you're talking about when you mention second order systems. However, Godel's incompleteness theorems (plural) were a lot more general than you're suggesting.
First Theorem:
"Any effectively generated theory capable of expressing elementary arithmetic cannot be both consistent and complete. In particular, for any consistent, effectively generated formal theory that proves certain basic arithmetic truths, there is an arithmetical statement that is true, but not provable in the theory."
Second Theorem:
"For any formal effectively generated theory T including basic arithmetical truths and also certain truths about formal provability, T includes a statement of its own consistency if and only if T is inconsistent."
It wasn't that Godel proved that Peano arithmetic was incomplete that shocked mathematicians, it was that he showed that _no formal system_ could ever be complete as long as remained consistent.
Of course maybe this second order system isn't consistent, in which case there's no problem. After all, I'm fairly convinced that human reason isn't always perfectly consistent, so it makes sense that we can avoid Godel's theorems. Of course, I see no reason we couldn't make a slightly inconsistent computer either.