Always route the traffic where you can. Only stretch vlans between sites when you absolutely have to (legacy multicast apps etc)
There wont be a routing loop, but you may see equal cost load balancing, and in these situations, I like to change the cost so that one circuit is always preferred.
Will the 2 links between the sites be equal in terms of latency and bandwidth? If they are the same, you could use both links, however the CEF switching engine is responsible for choosing the next hop based on source destination ip's etc, and it may not be the same in the reverse direction, but depending on what your traffic flows are between the sites, this may not matter at all.
If the links are exactly equal (are the fiber runs similar in length etc) Also think about bundling the links into an etherchannel, to simplify routing. Either layer 2 with Vlan interfaces on each end, or layer3 port-channel. Etherchannel does the assemtry work for you, as according to cisco (I haven't tested this on many platforms) etherchannel ECLB guarantees that return traffic takes the same path as the initial traffic flow.
Hopefully LACP frames will make it over the links. Otherwise you should route both links seperately.
