The problem is that it doesn't take much computer before the fact that the halting problem is theoretically solvable doesn't matter much. The Commodore 64 had 524,288 bits, which means even ignoring the other hardware that could have its own states it has 2^524288 states, approx. equal 10^157,828 states. You can't fit a record of all of the states that it might pass through in our universe. And it gets exponentially worse with every bit you add. An impoverished computer with a mere gigabyte of RAM would be 10^2,585,827,973 states.
So while in theory our computers are state machines, in practice we are much better suited to using the tools of Turing machines to analyze their behavior.
(I'm pretty sure you could construct an argument using the usual formulation of the halting problem to prove there is no practical easier way to tell that a computer will halt in general, but it would be more involved than I can sketch out. There is more to it than just swapping out "Turing machine" for "Turing machine limited to a tape of size X" everywhere.)
(Edit: Incidentally, I skimmed over the article the first time, assuming it was based on this observation. Deeper reading shows that it doesn't mean this, and in fact I don't actually know what it is intending to say, honestly. But the above still holds. Technically, all computers are state machines, not Turing machines, as Turing machines don't fit in our universe.)
You can model the state transitions as a linked list and use Floyd's classical tortoise and hare algorithm to (eventually) determine a cycle exists. Initialize "tortoise" and "hare" as two copies of initial state and advance hare by two instructions and tortoise by one each iteration. A cycle is reported if the two states become equal again.
A cycle of n instructions starting at instruction n0 will be detected in between n0 and n0+n iterations (i.e. <= 3*(n0+n) underlying instructions) since n0 iterations gets both into the cycle and the offset between them will become 0 some time in the next n iterations.
n could be very large, of course (e.g, using all of memory as a giant counter so the cycle length is huge), but the cycle detection is not really making your problem worse.
In this case, I'll back it down to suggesting there's probably some way to prove it can't be done without some unreasonable amount of at least one of time and space.
Put another way, you can simulate a nondeterministic Turing machine with a deterministic one, just as you can simulate a nondeterministic finite-state machine with a deterministic one. However, this simulation does come with increased time and space requirements.
This also has nothing to do with P vs NP