It is possible to method of getting round the 1024 byte key size limitation in MySQL? Essentially this really is leading to havoc when attempting to perform a compound index.
As I hesitate to point out that you are doing a problem (since i have not have the full particulars), it's rather unusual for any single key (a multi-part key) to become that large. I have seen tables in which the aggregate of all secrets on the table could be large, but rarely just one key.
The entire reason for secrets is by using a comparatively small area of the row to rapidly locate that row. If you are getting to the stage where your secrets are substantial, you most likely need to step away and re-examine the reason why you want them that large.
Your best choice is always to publish the schema here therefore we can suggest options.
Should you really do need secrets as huge as that, you might find that the only alternative would be to change to another DBMS. For instance, DB2/z comes with an 8K limit for every key. I am not recommending you attempt to buy a mainframe here, it is simply this is the only DBMS I understand the limits for off the top my mind - clearly you should think about a DBMS that isn't likely to cost a few million dollars to implement :-)
You can hash you values using crc32, MD5 or similar, then index the hash.
You should add an additional compare from the original area inside your SQL to cope with collisions but that wont set you back greatly as collisions are very rare.