Stewart Regan has rejected the notion that has undermined the Scottish FA's judicial panel.
Lord Glennie ruled at the civil court that the ban imposed on Rangers by the SFA's independent tribunal was unlawful and outwith the organisation's powers.
"I think the judicial panel has been proved to be robust," said SFA chief executive Regan.
"Different legal brains have different interpretations."
The judicial panel served Rangers with a fine of £160,000 and banned the club from signing players aged 18 and over for a year.
When Rangers' appeal was rejected by the appellate tribunal chaired by Lord Carloway the club chose to take the matter to the Court of Session in Edinburgh.
On that occasion, Rangers were successful and Lord Glennie decided the matter should be returned to the appellate tribunal for them to decide on an appropriate punishment for bringing the game into disrepute.
Regan dismissed the suggestion that a "deal" could be struck between the club and the SFA.
He said: "As a board, we recognise the independence of the process and we will not interfere.
"There won't be and can't be any deals, as has been highlighted in the press recently.
"There is no need for guidance as such. In terms of the appellate tribunal themselves, they will deal with the matter as they see fit.
"It is an independent tribunal.
"Our view is that football will govern football disciplinary matters. We will not go any further in the process.
"We will follow Lord Glennie's decision."
Regan says the SFA will not consider additional sanctions against Rangers for taking their case to the civil court, and not to the Court of Arbitration for Sport.
"There is a consideration that we have within our articles where going outside of the Scottish FA's articles and going to a civil court technically could have breached the Scottish FA's articles," he said.
"However, in light of Lord Glennie's comments and having discussed the matter with Fifa, it is not our intention to take any action.
"We are aware of the reasons why Rangers did what they did and we will not be pursuing them for that."
And on the involvement of FIFA, Regan added: "We have had communication with Fifa over the last week.
"As of this morning, we have received a fax back from Fifa confirming that the Scottish FA are not in breach of Fifa statute 64.3.
"They are very happy with the fact that the Scottish FA are managing this process.
"We have kept them in the loop right from the outset and they have got no further action that they are intending to take."