Some excellent legal points raised here by 'someone'.
Without knowing how this situation arose and why the company chose to pay into an employees SIPP rather than the company scheme it's difficult to determine where the liability is. In my experience, it is unlikely that the receiving scheme (SIPP) has had any unauthorised contributions, providing the payments fell within the members AA etc, even if it exceeded the AA the SIPP provider is likely to have identified this and offered options for paying any additional tax lability. The issue here clearly isn't AA related anyway.
I would assume the liability is with the employer. Why did they agree to pay into the SIPP? Surely it would be down to the employer to know their own company rules and not the employee. Is it perhaps that the employee was in a senior position within the company and asked for the payments to be made separately to the company scheme? If that it true I would still argue that the liability should be on the company to check first.
I have never know a situation like this and I suspect it is very unlikely that the SIPP provider will facilitate a withdrawal without advice. Normal rules would apply to any withdrawal and beyond that there are other major issues here. Withdrawing from the SIPP, even to rectify an error could have a devastating impact to the future benefit of a SIPP. MPAA rules may apply restricting future contributions and that's on the assumption the member is over 55 in the first place.
You mention that the funds were invested into commercial property. If so, it is possible, likely even, that the SIPP has liquidity issues, you can't just sell half a building. If the SIPP contains commercial property funds then again, liquidity issues may be present as some of the major funds have been suspended due to both Brexit and COVID-19 issues, when they reopen is will also be expected that there will be additional cost for withdrawals (to try to negate the mass rush to withdraw).
An actuarial calculation of what was invested, charges applied, investment returns and changes within the SIPP would be needed and this is an enormously complex, bordering on impossible calculation.
I would argue the only real practical solution here would be to fund the payments from external assets, again, on the assumption they exist.