Regex-based with str.replace
This regex pattern with str.replace should do nicely.
s.str.replace(r'\.(?=.*?\.)', '')
0    1234.5
1     123.5
2    2345.6
3     678.9
dtype: object
The idea is that, as long as there are more characters to replace, keep replacing. Here's a breakdown of the regular expression used.
\.     # '.'
(?=    # positive lookahead
.*?    # match anything
\.     # look for '.'
)
Fun with np.vectorize
If you want to do this using count, it isn't impossible, but it is a challenge. You can make this easier with np.vectorize. First, define a function,
def foo(r, c):
    return r.replace('.', '', c)
Vectorize it,
v = np.vectorize(foo)
Now, call the function v, passing s and the counts to replace.
pd.Series(v(s, s.str.count(r'\.') - 1))
0    1234.5
1     123.5
2    2345.6
3     678.9
dtype: object
Keep in mind that this is basically a glorified loop. 
Loopy/List Comprehension
The python equivalent of vectorize would be, 
r = []
for x, y in zip(s, s.str.count(r'\.') - 1):
    r.append(x.replace('.', '', y))
pd.Series(r)
0    1234.5
1     123.5
2    2345.6
3     678.9
dtype: object
Or, using a list comprehension: 
pd.Series([x.replace('.', '', y) for x, y in zip(s, s.str.count(r'\.') - 1)])
0    1234.5
1     123.5
2    2345.6
3     678.9
dtype: object