They would be wrong. Anyone who has enough resources to get a proposition on the ballot has enough resources to get the legislature to pay attention to them. And something like prop 35 would pass in the legislature for the same reason it passed at the ballot box. But the legislature can make amendments.
For whatever reason it was included, however, as an individual voter, if you are for "increased punishment for human trafficking" but against that smaller part about sex offender username registration, you don't really have anything you can do other than decide "on the balance".
(To be clear, I went into this in more detail, as I think you were interpreting me to say that the sex offender registration part was the way to push through the human trafficking change: I was attempting to imply the reverse, although I think the argument stands even if the parts are just considered related to many people, as you still must decide what to do if you agree with the first half but disagree with the second half.)
As a specific example where I had to do this, I was for the changes being proposed to the California nexus tax formula that were on this same ballot, but was not certain if I agreed with having a large percentage of that new corporate income tax be earmarked specifically for clean energy (locking it away from education, infrastucture, or any number of other number of things it could be used for). However, as that part had a limited time horizon (five years), and as I felt the other change made sense, "on the balance" I decided to vote for that proposition.
Too many people fall into the trap of believing "we must do something; this is something; therefore we must do this."
In some cases, (as some might argue is the case with 30 this year; I live in a town that is pretty much just a giant University, so I have gotten tirade after tirade about education funding), delaying by another year may also be too painful to bear for many people: some kind of relief, at least for them personally (as they are themselves voters, so imagine them making this choice for themselves at the ballot box) is required now, or you may as well just give up and not bother.
I mean, imagine if your choice were (combining the tradeoff I expressed for 39's largely innocuous energy funding clause with the despair many people felt surrounding 30) "vote for this thing that will continue to fund your profession as a lecturer and will keep college tuitions low enough that you will be able to afford to keep paying for your kid's education" or "vote no, get laid off, and tell your family things will be tight this year, all because someone threw in a rider that directs some of the funds to something you thought wasn't even bad, and probably needed funds anyway, but wasn't the most efficient way the money could have been spent"... would you seriously vote no? Would you judge someone else who did?
When it comes to the latter, the litmus test I use is, "Is there a clear and urgent need for this law?" In this case, as horrible as human trafficking is, I do not believe that prop 35 passes muster on those grounds. Bear in mind that we're not talking about going from "no penalties for human trafficking" to "some penalties for human trafficking". It's going from significant penalties, to even more severe penalties. There is no urgent need for this law, and therefore no justification for skewering civil liberties.
In retrospect, though, the chances of all that happening conditional on prop 35 failing might not be enough to justify my original comment, even though each step is individually likely, since it requires 3 things to go right (and people often overestimate the probabilities of highly conjunctive events).