This is certainly a strange predicament to be in.
I'll do my best to try to help you out, but I don't work for AA.
Technically, AA is not responsibly for the Aloha Airlines portion of your trip. The money, for that portion of the trip (those flights on Aloha), would have gone to Aloha, which is why AA cannot refund it - even though you purchased it through AA.
There is something called a fare calculation code, which is basically the fare of each segment that you will fly. The total of all of the segments equals the total cost of the ticket (fare). The portion on Aloha, from Kauai to Honolulu, for example, would be a segment. You need to find out how much that portion of the fare was, per passenger. You then need to call your credit card company, with documentation of this (that you can get from AA, or may already have, if you have the itinerary, and reciept), and have your credit card company refund that portion of the ticket, since Aloha went bankrupt. -- this is assuming you paid by credit card. If you paid by check, or some other form, the below link may help you.
This may help you ---
http://www.alohaairlines.com/aloha_oe_faq.html
As far as your options, for another flight, unfortunately, you will have to purchase seperate tickets, for that, or, use the money, if you are able to get that portion refunded, to pay the change fee to have AA do it.
About AA changing your flights. Flights are subject to change, but they are supposed to notify you, if they make a change.