I transferred some ether form an exchange site to an invalid address (invalid in that the correct address was trailed by 6 numbers I accidentally pasted in). Looking for that address on Ethereum chain explorers I am told that is invalid. Will the blockchain refuse the transaction and return the funds?
Depends on "how" invalid it is.
If you send ether to a public address that does not exist (i.e. nobody has the private key for), assuming that the format of the address is correct (hex, correct length, etc), the funds are cryptographically unretrievable. The Blockchain sees it as a valid transaction but there is no private key so nobody can sign a transaction with that account as the sender. If you replaced the last 6 characters of the address with 6 random characters this would be the case.
If you paste an extra 6 characters at the end of a valid address, it no longer matches the expected format (length) of an Ethereum address, therefore it will (hopefully) be rejected by the wallet. The transaction will not be processed and all ether will stay in the sender account. If you did this, it is possible that the transaction did not go through but the exchange is showing that it did. Depends on how well the exchange tracks transaction confirmations. The best way to test what happened would be to type your address into a blockchain explorer such as etherchain.org and see what the actual balance is on that address.
When using an exchange, there's quite a bit of trust involved, for example users expect that the exchange will send the user-specified address, the user-specified amount of Ether.
In this case, where the user-specified address had 6 trailing numbers, what happens is determined by the code that the exchange is running. An exchange could easily detect that the address is too long and give the user an immediate error message: this is probably desirable. Or an exchange could ignore the 6 trailing numbers, and send to the resulting address: there are risks to doing this as @Raine mentions. Those are just some of the options for what an exchange could have implemented.
Ultimately, "are funds returned" is an issue between the user and exchange: blockchain transactions are immutable and non-repudiable, but an exchange can also reimburse a user if it desires.