I think the tools fill different purposes, so integration with JSIL is absolutely a possibility in the future. I did not do any speed comparisons, I just translate what you write in C# to the equivalent script, so if you write a fast script it will be fast, if you write a slow script, it will be slow :)
Well, how you create data structures might matter for performance - if you turn C# structs into JS typed arrays for example and do the proper conversions, that could be much faster than simple JS objects or even arrays.
Another question, did you do any performance comparisons of Saltarelle? (to normal C# builds, to JSIL, or anything else?)