A Merkle inclusion proof is a proof that a transaction is included in a block with a particular hash, nothing more. Whoever gave you that proof can lie by omission (claiming no transactions you asked for exist in the given block), but if a proof is given, it can be validated.
As I believe you realize, the proof only covers the inclusion of a transaction in a given block. It doesn't prove anything about that block itself. You must independently acquire information about that block and ascertain it is part of the currently best active chain. If you just ask some node what their best chain is, they can claim whatever, and you're trusting that node entirely. That is however not how you're supposed to use such inclusion proofs (unless you have reason to trust them, e.g. because it's your own node, or because it's run by a known entity that you're willing to rely on).
Instead, you (the verifier) would generally run a lightweight network node, which does some part of the network validation. It would connect to multiple other nodes, download the block headers from those nodes, and validate them (just their syntactic correctness and proof-of-work). Among the headers chains you received, you'd pick the most-work valid one, and then verify the Merkle proof against that.
There are still ways in which you can be cheated, but it's not as simple as a single node lying to you:
- Since you are only validating the headers, it is possible that the highest-work headers chain is not actually a valid blockchain (e.g., it could contain unauthorized inflation, theft, or double-spending). Doing so would not convince full nodes, but it can convince lightweight nodes. The theory is that attackers will not try this because it is expensive, hard (needs a majority of the hashrate to keep up), and hopefully a sufficiently important part of the ecosystem would not accept their blocks, thus making the cost of mining wasted. However, this assumption does rely on the presence of enough fully-validating nodes in the network to make the attack uneconomical. If you are concerned about this, your own option is running your own fully-validating node instead of a lightweight one.
- If all peers you talk to are attackers (or colluding with an attacker), something referred to as an Eclipse attack, and are thus shielded off from the real best chain, attackers can get away with constructing an alternate minority-hashrate chain, and hiding the real best chain from you. Depending on how long they can keep the Eclipse attack, this may still be extremely expensive.
Note that "majority of nodes" is never relevant in this analysis. The criteria are whether you have at least one honest peer, and whether a majority of the hashrate is working with the attacker.