(crossposted from stackoverflow)
Being in a situation that forces you to use the wrong tool for the job is not really "a good reason", in my experience.
I already explained (see below, in the comments) why it's not that bad of a choice. Also, I'm volunteering my time to this project: I have to stick with the solution that works, is easily maintenable and doesn't add further dependencies. Hopefully this can help understand why JS in this case is the right tool for the job.
I must say that I agree with Neil. Even after having read the comments below, I cannot see a good reason why you would need to run something in a web browser, yet not have access to use web services.
Because it's not a web browser. It's something built on top of the same platform (xulrunner) as Firefox but it's not a web browser. And, besides, the user base would probably be too big for anything less than a whole data center to handle. Now, if we could all go back to the question...
Also, keep in mind (as I already wrote below) I'm not talking about bioinformatics here: the sequences I need to align are not DNA/protein/codons sequences. They are generic sequences, and I'm almost sure that none of the servers you're talking about would 1) accept arbitrary sequences 2) allow me to use their computing power for something totally unrelated to bioninformatics.