I would construct the regular expression for the intersection, then convert to a regular grammar in normal form, and see if it's the empty language...
That seems like shooting sparrows with a cannon. Why not just construct the product automaton and check if an accept state is reachable from the initial state? That'll also give you a string in the intersection straight away without having to construct a regular expression first.
I would be a bit surprised to learn that there is a polynomial-time solution, and I would not be at all surprised to learn that it is equivalent to the halting problem.
I only know of a way to do it which involves creating a DFA from a regexp, which is exponential time (in the degenerate case). It's reducible to the halting problem, because everything is, but the halting problem is not reducible to it.
If the last, then you can use the fact that any RE can be translated into a finite state machine. Two finite state machines are equal if they have the same set of nodes, with the same arcs connecting those nodes.
So, given what I think you're using as a definition for orthogonal, if you translate your REs into FSMs and those FSMs are not equal, the REs are orthogonal.
That's not correct. You can have two DFAs (FSMs) that are non-isomorphic in the edge-labeled multigraph sense, but accept the same languages. Also, were that not the case, your test would check whether two regexps accepted non-identical, whereas OP wants non-overlapping languages (empty intersection).
Also, be aware that the \1, \2, ..., \9 construction is not regular: it can't be expressed in terms of concatenation, union and * (Kleene star). If you want to include back substitution, I don't know what the answer is. Also of interest is the fact that the corresponding problem for context-free languages is undecidable: there is no algorithm which takes two context-free grammars G1 and G2 and returns true iff L(G1) ∩ L(g2) ≠ Ø.