A spokesman for Beattie Media stressed it was Kevin Reid's own decision to leave.
Mr Reid was secretly filmed with a colleague by a newspaper, which reported that the company said it could provide access to government ministers.
The Scottish Parliament's Standards committee has published its final report on the affair, which cleared ministers of any wrong-doing.
No evidence was found that any MSP had breached any code of conduct.
But the report expressed concern about a conflict between the evidence of Alex Barr, an employee of Beattie Media, and Christina Marshall, the secretary of Finance Minister Jack McConnell, who was at the centre of the most serious allegations.
The committee's remit only extends to MSPs and its investigation can go no further.
It will now focus on drawing up a code of conduct for MSPs which will include appropriate safeguards against the influence of lobbyists.
The report also recommends the Ministerial Code of Conduct should be re-examined as it makes no reference to lobbyists.
Negotiations are under way to appoint an independent commissioner for parliamentary standards.
The move won widespread support when proposed last month as it would allow allegations against MSPs to be vetted by a legally-trained official, to weed out the trivial, malicious or politically motivated claims.
The standards committee would still have authority to investigate allegations of a serious nature, but a process of pre-scrutiny, similar to the one which operates at Westminster, would ease the committee's workload.