The alternative to using total number of points is to do it by percentage of points taken. So team that's played 3, with 2 wins 1 draw = 7 points, is put above someone played 6, 3 wins = 9 points.
Premier Division1 Heriot-Watt University 83%
2 Edinburgh City 77%
3 Dalbeattie Star 76%
4 Lothian Thistle 57%
5 Spartans 55%
6 Preston Athletic 44%
7 Coldstream 38%
8 Edinburgh University 33%
= Whitehill Welfare 33%
10 Easthouses Lily 29%
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11 Selkirk 25%
12 Peebles 0%
First Division1 Gretna 2008 100%
= Stirling University 100%
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3 Tynecastle 83%
4 Gala Fairydean 60%
5 Craigroyston 55%
= Leith Athletic 55%
Eyemouth United 46%
8 Civil Service Strollers 33%
= Kelso United 33%
= Ormiston 33%
11 Hawick Royal Albert 4%
12 Vale of Leithen 0%
However, I don't think you can claim that's a full-proof method either... - it depends on who you've played, and clubs that have played only a handful of games get distorted more by 1/2 bad results.
Anyway, clubs with 8 games in hand just makes for more of the excitement

- doesn't it

...