I'm sure there must be an easier way than running another cable or rerouting the existing
Not really. As you have figured, the original upstairs thermostat wiring needs to be rerouted to pin 3 of the hub. However, installations vary from property to property and also according to the personal preferences of the original installer, the answer as to how to do it will depend upon that, but generally there are three options:
1. Extend the cable from the existing thermostat to the 3 channel wiser. Believe it or not this is usually the easiest and safest way for DIY.
2. Find where the original thermostat wire originates from, often a wiring centre maybe in the airing cupboard disconnect the existing thermostat from it and run a new cable to the Wiser from there. Although, that may be more difficult to do than option 1 depending on the layout of your home.
3. The Wiser hub can be located next to the wiring centre and wired to that to control both zones and the hot water from there, whilst it may be easier in terms of actually running the cables, a full understanding of what all of the wires inside the wiring centre do, and again this varies from property to property, and a lot of changes would need to be made, so generally not recommended for DIY, as there's a lot of scope for error.
I guess I could just run a spur off 1 to 3 but then it would not be a 2 zone system.
Not quite sure what you mean by that, if you mean link 1 and 3 together that won't do anything as the wiring controlling the upstairs heating will still be connected to the upstairs thermostat so that will continue to control the upstairs heating.
Apologies if I've misunderstood what you've said. However, if it's a newish build, the requirement for two heating zones was introduced, around 2010 as part of the building regulations (Part L) as a bid to save energy. The concept is that rooms that are in regular use when the property is occupied are on one zone, and the second zone is for bedrooms that are only generally used at certain times of the day, so don't need to be heated for as long.
If that's the case with your home, converting it to a single zone would put it in contravention of the regulations, although I can't imagine anyone will check, but it might cause a problem in the future if it's picked up in a survey when the property is sold.