It is not unusual for a “disqualified person,” which includes founders and directors, to rent property to a 501(c)(3) public charity without incurring an improper private benefit.  (I assume the (c)(3) is a public charity because any lease between a private foundation and a director is a taxable self-dealing transaction.)  So long as the rent is reasonable, it will not result in an excess benefit subject to tax.  Independent members of your board should assure that the relationship is reasonable. (See Ready Reference Page:  “Charities Must Avoid Excess Benefit Transactions.”)

With grant-funded improvements to the property, you can probably protect yourself by assuring that the charity has the right to use the property for the full depreciable life of the improvements and by providing that you will repay it the undepreciated portion of the improvement cost if the lease terminates before the depreciation is completed.

I am more concerned with moving additional historic buildings onto your property.  While there is a theoretical depreciation date for all real estate (other than land), as a practical matter, buildings, and perhaps particularly historic buildings, can retain some significant value after the end of the theoretical depreciation.  Your best bet to protect yourself here may be to give the charity long-term access to the additional buildings and repay the charity the relocation costs, perhaps over time if necessary, with interest.  You should be sure you have the approval of the grantmaker for the arrangement. 

I would be interested in hearing whether readers have any other suggestions.