At the SRU AGM at Murrayfield, bosses insisted Scottish rugby was in good health after McKie's departure on June 14.
Senior non-executive director and former international Jock Millican replaced McKie on an interim basis and said the recruitment process for a permanent chief executive has begun.
Millican, who described the last two weeks as "a steep learning curve", praised McKie for enabling a smooth transition into the role and insisted the recent departure was merely a blip.
Millican said: "We've changed the person at the top, that's all. Everyone else that's in place is still there.
"It is not a great problem. Yes, there's been a stutter but we'll be moving again very quickly.
"It is a challenging time. There are issues we've got to address and they will be addressed and taken forward, but Scottish rugby is in very good health."
Earlier this month the SRU denied reports of a power struggle within the organisation.
A board meeting was held on June 9 amid claims that McKie had been under pressure from members over the direction of Scottish rugby, particularly over the decision to freeze the playing budgets of Magners League sides Glasgow and Edinburgh.
However, the SRU had insisted there was unity among the 11 board members.
Outgoing chairman Alan Munro, who is to be succeeded by Sir Moir Lockhead, said: "The past month or so has been most regrettable.
"Despite this and despite some media comments, I would like to thank Gordon McKie, (finance director) Eamon Hegarty and the entire staff here at Murrayfield for their outstanding contribution to Scottish Rugby.
"The organisation today is transformed from the shambles that I walked into six years ago and I believe their effort should be recognised."
Munro was making reference to McKie's input during his six-year tenure, particularly when discussing financial improvements.
For the last financial year, the Scottish Rugby Union increased turnover to £35.1million and yielded £1.3million surplus.
Scotland had three home autumn internationals - the win over South Africa taking them to a high of sixth in the International Rugby Board world rankings - and three home matches in a disappointing RBS 6 Nations campaign, contributing to the financial results.
The SRU pledged to increase the funds injected into grassroots rugby from £1.7million last year to more than £1.9million next season, while announcing their intention to field a full-time sevens team in the IRB World Series.
Ian McLauchlan was re-elected unopposed as president, while Alan Lawson was elected as vice-president.
Successful motions included the restructuring of the domestic league and cup competitions and the establishment of a Scottish rugby museum at Murrayfield.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The Barbarians are one of the top invitational rugby sides with a long history and classic rugby jersey.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Lions get ready for their matches with this green training jersey. It's what the players wear. Get in the Gear!
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The Lions are ready to get their Australia tour underway. They arrive in Perth on Monday.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.