Your main course of action here should be via your travel agent, but first of all you need to understand if what you booked via them is classed as a "package", or if the agent dynamically packaged (booked the flight & hotel seperatly via different providers) the arrangements on your behalf...
The key here is that if you believed you were buying a package (ie you advised the agent of your requirement - 4 night stay in Las Vegas) you are covered under the package holiday regs, and will be covered for both flight & hotel/transfers if applicable. If however the agent booked the arrangements via 2 seperate suppliers and you knew this, then you are not covered by the package regs.
An easy way for you to figure this out is if your invoice/quote from the agent gave you the cost as a combined total (ie £800 p/p for VS flights and 4 nights at the XXX hotel), as this would be deemed as the agent having supplied a package under the EU regs (note - some agents will dynamically package as this is generally cheaper - BUT if they do and then give the impression to you that you have bought a package they are liable) - also worth noting here that if the agent has done this, then they should have sold the trip under an ATOL...
If however you recieved an invoice/quote from the agent which clearly shows that the flights & hotel have been purchased through seperate suppliers, and the cost for each is seperated, then this doesnt form a package under EU regs and you are up sh*t creek without a paddle as far as trying to get a refund/change of the hotel...
I worked in the tour operating business for almost 20 years, and VS are complying with their interpritation of the regs, to my knowledge it has never been proved in court either way.
In my opinion, you have a couple of choices:
1) Continue your battle with VS, but I doubt you will get anywhere.
2) Rebook with another carrier (you may wish to seriously concider this, as in my opinion VS do not offer the most comfortable seats in economy, and also their LGW fleet is way behind that of the LHR fleet in terms of decor/IFE etc. Also, although another carrier will not be direct, you may find that a break in the journey en-route will give you a chance to strech your legs, plus you will have cleared customs/immigration at your stopover point.
3)If you are determined to fly with VS, then speak to your agent about picking up the cost of the onward ticket (from SFO/LAX), as $49 may be a very cheap option to sort out what could be a major problem for them, depending on the above package/dynamic package argument.
Finally, given all of the work that you have put in, your agent hasnt really provided any service/value to you whatsoever - happy to take your money, but not happy to sort out when you have an issue!