If I remember correctly from the old forum, the starting and electrical systems are seperate so, if it's running fine without the lights, that should work just fine. I would think you only need the charging system for the lights, but utimately have not had this happen to my TW yet.
Of course, Idaho 5-0 may not like you driving it without the lights on the streets, but off road would be ok (guessing your not gonna ride in the dark anyway ha ha). Not gonna look it up, but I think there is a requirement for a headlight to be on when we drive on the roads. Older bikes with an on/off light switch may be exempt, but I don't own a bike old enough to qualify.
Oh, and you are a lucky dog having a kick starter, I'm jealous. Mine is an 05' and came without. Long range plan is to put one on, but not this summer! My battery died a few weeks ago, have to jump or bump start it. Haven't had time to buy a new one yet. Left it running a lot when I went on my Buck Park Cabin ride a few weeks ago.
P.S. Sending you Hemingway Butte map soon. Have to copy it to the CPU and haven't had time yet. Map on Idaho BLM site doesn't have the quality that I remember my printed copy has.