which one is better?

首先, 第一句句子係較好, 原因係

1) 佢係無錯的, 係報章的原文。
2) 佢用咗一個defining clause去提供跟subject有關的一些決定性資料, 令我地知道所提及的問題是那一個。

第二句句子運用了non-defining relative clause, 但第一個comma的位置應該係issue 和 on之間。致於用到non-defining relative clause, 我就覺得不適合, 因為這句relative clause的資料係決定性的, 如果沒有它, 我地根本唔知話題中的 the issue係指咩? 而Non-defining relative clause 的作用係提供subject的額外資料(但非決定性的資料, 簡單D講, 即係可有可無 i.e. nice-to-know information ), 但這個clause並非Non-defining relative clause。
diverge on <an issue>解作「在某問題上意見分歧」, on係不可以刪去, 但可以有兩個位置擺放, 一係跟第一句一樣, 一係好似以下呢句。

It seems that the issue which we have diverged on is more important for some than agreement as a whole.

Agreement可以無 an, 就正如以下例子中的 apple

I like eating apple everyday.
(我喜歡每天食蘋果, 無需有 an, 除非你要強調每天食一個蘋果, 甚至寫成I like eating one apple everyday.)

最後, 重寫句子:

It seems that we have diverged on this issue. However, the issue itself is more important for some than agreement as a whole.

似乎在這問題上, 大家仍然是意見分歧, 但是, 這問題本身比起我們是否意見一致還重要 (即是: 我們是否意見一致並不重要, 這問題本身才是最重要)。


圖片參考：http://tw.yimg.com/i/tw/ugc/rte/smiley_1.gif

the first sentence was found in a newspaper,
my question should be " how to split the sentence into few shorter ones"

It seems that the issue on which we have diverged is more important for some than agreement as a whole.
有關你兩句子的問題, 樓上的仁兄己解釋得很清楚, 我亦什同意, 如你要簡短及文法上正確, I suggest:
It seems that the issue we have diverged is more important for some agreements as a whole.
與你的句子一樣, 只是減了些不必要的字.

It seems that the issue on which we have diverged is more important, for some than agreements as a whole.
其實你第2分句係咪漏左個形容詞?應該係for some xx than agreements
It seems that the issue on which we have diverged is more important, for some is better than agreements as a whole.

It seems that the issue on which we have diverged is more important for some is better than agreement as a whole.
個結構令人唔想睇落去,因為太長,唔斷句.

我只可以話你知，你第二句o既grammer 係錯。

你用兩個逗號去分隔開 (which we have diverged)
係英文學上，兩個逗號分隔開又用which, who, where 等w 字開頭o既句子o既話，係可以唔睇。換句話o黎講，你句嘢就會變成

It seems that the issue on is more important for some than agreement as a whole.

咁你話係咪錯丫。

我知你厭第一句煩覆。想改簡單D，或者我試下

It seems that the issue, which we have diverged on, is more important for some that the agreement as a whole.

其實你第一句個grammer 都係錯...
應該係， the issue when we have diverged on.

仲有一個好minor o既mistake 想提一提
agreement, 任何字如果佢地唔係眾數，前面要跟a, an, the.
即係some than agreement 應該寫成 some than an/the agreement

另一個example..
apple: I ate an apple.
I ate apples.
永遠都唔應該寫成 I ate apple