You're ignoring that Thurrock had a better record than Stafford, hence why they are being reprieved. Had it been at team in BSN thrown out, then Stafford would have been reprieved.
I was aware of the reasoning behind it, and I suppose the Conference had to do what it had to do. But part of me wants to play devil's advocate here. Let's look at the statistics...
Thurrock Played 42, Points 37
Stafford Rangers Played 40, Points 32
(i) The two sides didn't play an even number of games. Technically Stafford still have two games in hand of Thurrock. These games are hypothetical, but let's consider that Stafford win them both. Which team then has the best record?
(ii) The two games in hand were against Ilkeston, who were unable to fulfill their fixtures. If Ilkeston had continued and perhaps fielded a youth team every week (much as Durham did in the Unibond League), then perhaps Stafford would have had six additional points.
(iii) Thurrock and Stafford didn't face each other competitively during the season. Nor did they face the same core group of opponents. In the absence of head-to-head competition between the two divisions, it is unsafe to assume that they are of equal strength. Is points-per-game therefore a fair yardstick? You might as well toss a coin.
Neither Thurrock nor Stafford could have any complaints about being relegated with the records that they had. So given the geographies involved and allowing common sense to prevail, a reprieve for Stafford would have maintained the geographical balance of the leagues and avoided the ridiculous level of travelling now imposed on Bishop's Stortford - who through no fault of their own are the victims in all of this.