The unity referred to in Scripture is a spiritual unity of everyone within the Body of Christ; that is, all who have received Him as personal Saviour.
This means that our unity must always be based on the truth of the Scriptures, which tell who Christ is and what we are in Him. Any unity that compromises the teaching of the Scriptures regarding Jesus Christ is not a unity that has God's approval.
However, the ecumenism of our day seems far more concerned about unity for unity's sake, than it does about adhering to the truth of the Scriptures.
In fact, the teaching of the Scriptures is sometimes de-emphasized so much that for the sake of unity some groups do not even have doctrinal statements.
Such groups tend to emphasize God's love and the need of working in harmony with those with whom we disagree. It is naive, however, to emphasize love at the expense of truth--to emphasize God's love but not His holy standards and justice.
Organizational unity is not necessarily wrong if only believers are involved. However, it is wrong--no matter how good the cause may be--for believers to compromise their message in order to work with unbelievers.
When Paul said we are to be "endeavouring to keep the unity of the Spirit," the word he used for "endeavouring" was a word that originally meant "to make haste" and then came to mean "to be zealous or eager, to give diligence."
Each believer is to give his utmost attention to see that harmony is preserved within the Body of Christ. It is a spiritual unity, or oneness, that exists among all who know Christ as Saviour, but it can be maintained only as we walk in fellowship with Him.
"Behold, how good and how pleasant it is for brethren to dwell together in unity!" (Ps. 133:1).