IT was the most controversial debate the SNP has had in recent times: whether to ditch its long-standing opposition to Nato membership.

The conference batted the issue back and forwards for two hours, and what a debate it was. Impassioned and at times heated, it was extended to allow more delegates the chance to speak and gave vent to a wide range of unalloyed opinion. It was proper politics, in short, a sadly unusual phenomenon in an age when party conferences are less about debate than about showcasing politicians.

The party leadership will be hoping that, having won the day, even by such a tight margin, the issue can now be put to bed and its energies focused on the big push towards 2014.

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In truth, however, the consequences of this tectonic shift in policy, for the party and for the pro-independence campaign, are not yet entirely clear.

It quickly emerged during the debate that, for many delegates, their opposition to supporting Nato membership for an independent Scotland was moral. Some gave emotional speeches reasserting their commitment to the removal of Trident from the Clyde and their belief that it was incompatible with membership of Nato. There was deep discomfort about the notion of changing policy in response to polling evidence showing 75% of Scottish voters supported Scotland remaining part of Nato. The language used – words like "dishonest", "hypocritical" and "unethical" – gave some indication of how wounded they felt.

Alex Salmond will want to believe that, given the greater prize of winning the independence referendum that is now at stake, party activists will pull together for the cause; the likelihood is that most will, but perhaps not all. There will have been some delegates nursing whiskies as well as their wrath in Perth pubs last night who were saddened at the thought that a Rubicon had been crossed, with principles, as they see it, traded for popularity. It remains to be seen whether that will dilute their campaigning spirit in the run-up to 2014.

Certainly, the vehemence of feeling on show, and the fact the leadership's amendment was almost defeated, was a reminder to Mr Salmond that he cannot take his party's support for granted, even this close to the longed-for referendum.

Then there is the question of how feasible the party's new position on Nato actually is. Many delegates yesterday voiced their worries over this point. Nato membership would make it harder for an independent Scotland to rid itself of nuclear weapons, warned MSP Jamie Hepburn.

German newspaper reports last month suggested that Nato had forced Germany to drop its aspiration to bring about the withdrawal of US nuclear weapons from its soil. Would any negotiation on the point even be possible? The assumption that it would, some opponents believe, is simply "policy by assertion". The pro-Union Better Together campaign, which was surely disappointed by yesterday's vote, will seek to exploit such doubts.

Ultimately, it was a day of victory for the party's leadership and a significant staging post on the road to the referendum in 2014. Opposition to Nato may have been one of the party's defining policies, but the other, bigger cause of independence ultimately eclipsed it. The credibility of the party's new defence policy must now be judged by the Scottish public.