I haven't fully tested this yet, but I believe if you insert a blank [tr][/tr] at the beginning of your table (but AFTER a table header, if present), it will alternate the rest of the rows light/dark instead of dark/light
A couple of examples, using Rawhide's tables from above:
Header with reverse alternating row colours
[table="width: 500, class: head alt1"]
Spoiler
111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111
Header with reverse alternating row colours, no inside borders
[table="width: 500, class: head alt1 outer_border"]
Spoiler
111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111 111111
This renders properly on Safari and Chrome. Haven't tested it on other browsers.