Yes, if you're a married couple with AGI over $310k or a single person with AGI over $258k, your itemized deductions will phase out a bit.
Seems like the obvious thing, if you want to avoid this, is to reduce your AGI. Max out all tax-deferred savings options: 401(k), HSA, SEP or solo 401(k) through your business. Harvest some losses in your taxable brokerage account. See if your W-2 job would let you take a month off, unpaid. Make more business expenditures that you may have been putting off. Consider hiring some people to work on the business, reducing your personal income and increasing your free time.
If you've done all this and still are over the limit, count yourself lucky and pay the tax.
As to whether this is a disincentive to charitable contributions, sure I guess it is. If the government makes you come up with 100% of the donation out of your own pocket instead of only 70% (or whatever), you'll perhaps donate a bit less. It is what it is.